The Alignment Trap: Why Your Best Leaders May Accidentally Work Against Each Other

The Hidden Architecture of Misalignment 

Here’s the thing about organizational crises, especially interconnected ones: They demand coordination across teams that normally work semi-independently. This creates what researchers call multiteam systems — networks of teams that must work together toward shared goals while maintaining their specialized functions.

During the COVID-19 pandemic, most organizational leaders initially saw it as a health crisis requiring medical expertise and safety measures. Within weeks, however, organizations had to coordinate emergency responses across teams that rarely worked together closely: IT teams supporting remote work, HR handling workforce safety, operations maintaining service delivery, and finance managing cash flow problems. The coordination challenges were immense — and many organizations struggled not because they lacked good teams, but because their leaders hadn’t developed the capabilities to navigate multiteam coordination under pressure.

This coordination challenge is so critical and pervasive among our clients that we conducted research applying multiteam systems theory to polycrisis conditions. Our research identified 5 critical coordination challenges that can emerge when multiple teams respond to a polycrisis — and multilevel goal alignment is the foundational challenge that amplifies all the others.

Most coordination frameworks fall short. They focus on getting teams to talk more, such as creating cross-functional committees or reorganizing reporting structures. But the fundamental challenge lies deeper: How do leaders maintain strong commitment to their team’s goals while simultaneously committing to broader system-level objectives?

The Differentiation Paradox Can Create Challenges With Organizational Alignment

As teams become more specialized — which they must do to handle complex challenges — they naturally develop stronger internal identities and priorities. Research calls this differentiation: the degree of difference and separation between teams.

Think about your organization. Your IT team develops its language, metrics, and ways of working. So does finance. And operations. And legal. This specialization is valuable — you want deep expertise. But it creates a differentiation paradox: The more specialized and cohesive your teams become, the harder it is for them to coordinate with other teams.

Why? Because strong team identity can create goal discordancy — when what teams are trying to accomplish in the near term (their immediate objectives) conflicts with what the organization needs to accomplish overall (especially during crisis conditions when overarching priorities must take precedence).

Consider how this plays out in normal business conditions: A product team launches an innovative feature that delights customers but creates massive support volume the customer service team can’t handle. A finance team implements cost controls that prevent the operations team from maintaining service quality.

None of these teams were wrong. They were each succeeding at their level — and accidentally undermining the whole.

The Solution: Balanced Identification

What makes this coordination particularly difficult for leaders is dual identification. Leaders must simultaneously:

1. Maintain strong identification with their team, and
2. Develop equally strong identification with the broader multiteam system

This isn’t just about keeping both in mind. It’s about building genuine commitment to both levels. And here’s the trap: focusing too heavily on either level undermines the other.

Over-identify with your team, and you get the scenario we opened with — brilliant local optimization that creates system-level chaos. Your leaders become so committed to their team’s success that they lose sight of how their decisions impact others. Research shows this leads to increased inter-team competition precisely when collaboration is most essential. 

Over-identify with the system, and you get a different problem: leaders so focused on system-wide goals that they neglect critical team-level processes. Studies have found that too much between-team communication reduced team members’ identification with their own teams, weakening the units the system depends on.

The solution is balanced identification: developing leaders with the situational awareness to know when to lean in which direction. This doesn’t mean constant dual focus at equal intensity.

Think of it like emergency response coordination. When a crisis first hits and your team is in the hot seat, that’s when system-level coordination demands peak attention. Your team must step up, coordinate intensively with other teams, and defer some local goals to support systemic imperatives.

But that intensity can’t be sustained indefinitely. Once the critical phase passes, leaders need to recognize when it’s time to lean back into team-level focus — to rebuild team cohesion, address deferred team priorities, and restore the team identity that got depleted during the crisis push.

The leaders who navigate this well aren’t trying to always maintain perfect balance. They’re developing the discernment to shift focus appropriately as conditions evolve.

The New Urgency of Multilevel Organizational Alignment

Balancing team and organizational goals isn’t new. What’s new is the intensity and complexity of today’s disruptive operating environment, driven by 2 fundamental changes:

First, the pace and interconnectedness of crises has intensified. A decade ago, organizations typically faced crises sequentially — a market disruption, then an operational issue, then a talent challenge. Today’s polycrisis conditions mean these crises hit simultaneously and interact in ways that amplify each other. When economic shocks intersect with environmental events, technological disruptions, and geopolitical risks, the coordination challenges multiply exponentially.

Second, resource conflicts have become more acute. When multiple crises compete for the same specialized teams or expertise, leaders face increasingly difficult allocation choices. The same engineering team might be critical for both your digital transformation initiative and your sustainability compliance efforts. How does the leader of that team balance those competing demands? It requires systems thinking to understand the cascading implications of each choice and situational awareness to recognize which crisis demands priority at different moments.

Without capability development at the multiteam coordination level, the answer typically defaults to whoever has more organizational power — not what’s strategically optimal.

Here’s what our research shows: Organizations that develop multilevel coordination capabilities don’t just survive polycrisis conditions — they find breakthroughs. When specialized teams successfully balance component-level and system-level commitment, research shows they demonstrate greater creativity and achieve better outcomes than teams that over-identify with either level.

Our case study on telemedicine accessibility during the pandemic illustrates this: Specialized teams across information technology, regulatory frameworks, social dynamics, and economic structures collaborated to achieve breakthrough innovations. This wasn’t just about responding to a health crisis — it was about multiple teams maintaining their specialized expertise while coordinating toward a shared goal that none could achieve alone.

What drove this coordination? Not pre-existing competencies, but unavoidable necessity. When the pandemic hit, healthcare leaders didn’t need to recognize that telemedicine required cross-team coordination — the crisis made single-team solutions impossible. IT systems failed without regulatory flexibility. Virtual care couldn’t scale without reimbursement changes. The coordination imperative was forced by circumstances, not chosen through strategic insight.

This raises a critical question for organizational leaders: Can you develop the capability to coordinate across teams before a crisis makes it unavoidable? That’s the leadership development challenge.

Our Framework To Make Multilevel Alignment Practical

How do you develop multilevel coordination capabilities? Our Direction – Alignment – Commitment (DAC)™ framework provides a practical structure.

Direction means fostering understanding and acceptance of shared multilevel goals across all teams. This sounds straightforward but requires nuance: leaders need agreement on system-level goals while maintaining clarity about how their team-level goals connect to and support those broader objectives. This becomes challenging when different teams have different goal priorities and compatibilities across the system structure. It becomes even more challenging in polycrisis conditions, when system-level goals may be forced to shift quickly.

Consider what happens during a major system integration after an acquisition. IT teams focus on technology infrastructure and data security. Finance teams concentrate on reconciling accounting systems. HR teams prioritize benefits harmonization. All are working toward successful integration, but each team defines success differently. The organizations that achieve smooth integration are those that get specific about what success means at both the team level and the system level.

Alignment ensures that all teams understand how their contributions connect to overall success — and critically, how those connections must be maintained as roles and priorities evolve during complex challenges. This is where the multilevel nature becomes most visible. Leaders need to see not just how their work contributes upward to system goals, but also how their decisions impact laterally across other teams.

Commitment involves building a willingness to exert effort for both the component team and overall system success. This is the piece that gets most neglected in traditional organizational alignment efforts. You can’t just tell leaders to care about the whole organization. You must create conditions that make that commitment psychologically sustainable.

Leaders can develop this dual commitment through:

• Establishing clear connections between component and system goals so leaders understand how their work contributes simultaneously to both
• Creating structures where teams participate in setting their goals while understanding alignment with system-wide objectives — fostering dual identification through bottom-up decision making
• Facilitating processes where team leaders help members build connections to both their immediate team and the larger system through structured activities
• Implementing communication patterns that equally reinforce both team identity and system identity
• Creating clear guidelines for adaptive focus shifts, so leaders recognize when crisis phases demand intensive system-level coordination versus when to refocus on team-level rebuilding 

Closing the Cross-Functional Alignment Gap: Why Leadership Development Is Key

Here’s where this becomes a leadership development challenge rather than just a structural one: You can’t redesign your way out of the multilevel alignment trap. You must develop your way out.

Yes, you need the right structures — cross-functional teams, clear escalation paths, communication protocols. But research on multiteam systems shows that structure alone fails without the leadership capability to navigate it. Leaders need to develop:

• Cognitive complexity to hold multiple goals and identities simultaneously
• Systems thinking to understand how decisions cascade across team boundaries
• Boundary spanning skills to effectively coordinate with other teams
• Adaptive decision-making to know when to optimize locally versus systemically

This is why traditional approaches often fail. Organizations create cross-functional steering committees (structure) but don’t develop the multilevel coordination capabilities those committees require (development). They establish communication protocols (process) but don’t build the skills to in order to use them effectively (capability).

Effective organizations take a developmental approach:

Start with assessment and shared understanding. Use tools like multiteam system mapping to help leaders visualize current interdependencies and identify where coordination patterns need to shift. When leaders see the full system, they begin to understand the multilevel nature of their work.

Create shared developmental experiences. Research shows this develops when teams engage in shared experiences that foster growth together. This might mean scenario planning exercises where cross-functional teams practice navigating polycrisis conditions, building shared mental models about when and how leadership should shift.

Foster psychological safety and collective efficacy. Leaders are more willing to assume broader system leadership roles when they feel psychologically safe to do so. They’re more likely to accept others’ leadership emergence when there’s collective efficacy — shared confidence in the system’s ability to lead effectively.

Make the invisible visible. Give leaders language for what they’re experiencing. When a team leader can name the dual identification challenge and recognize that the tension they’re feeling is a normal part of multilevel coordination, they’re better equipped to navigate it skillfully.

Embrace organizational learning. Following a major disruption, make the time to encourage collective sensemaking through after-action reviews. The best way to learn is through experience, and crises can be a pressure cooker of fast-paced learning in organizations. To adapt and level up, leaders need the time and space to understand what went wrong and imagine a more effective future state, both within their teams and across the system. 

Developing Leaders for Multilevel Coordination

Most organizations have more leadership capacity than they realize, but it’s trapped at the wrong level. You have strong team leaders optimized to excel at team-level performance, but their multilevel coordination capabilities may remain undeveloped.

This is the opportunity. When you help leaders develop balanced identification — genuine commitment to the polarity of both their team and the broader system — you harness capabilities that your organization desperately needs for navigating complexity.

Research shows that leaders with balanced identification facilitate greater creativity in multiteam systems. When leaders maintain genuine commitment to both levels, they’re better positioned to see opportunities for innovation that span team boundaries, make decisions that optimize systemically rather than just locally, and model the kind of leadership that helps their team members develop these capabilities too.

5 Questions for L&D Leaders & the C-Suite

These 5 questions will help you assess your organization’s alignment:

1. When you ask leaders to articulate how their team goals connect to system-level objectives, what do you hear? Are they vague statements about the company mission or specific, causal links?
2. Do your high-performers show signs of over-identification with their teams? Are they optimizing locally in ways that create systemic problems?
3. Have you created developmental experiences that build multilevel coordination capabilities? Or are you just creating cross-functional structures and hoping leaders figure it out?
4. Do your leadership competency models include multilevel coordination capabilities? Or do they focus primarily on leading single teams?
5. Can your leaders recognize and navigate the dual identification challenge? Do they have language for what they’re experiencing and frameworks for managing it?

The organizational alignment trap is real, and it’s costly. But there’s also opportunity: Your leaders aren’t failing to collaborate. They’re succeeding at the wrong level of the system — and that’s a development gap you can close.

The organizations that will succeed in polycrisis conditions aren’t those with the smartest individual teams. They’re the ones that develop leaders capable of coordinating across teams, balancing dual commitments, and prioritizing the systemic view even when it creates local tension.

That’s a leadership development challenge. And unlike the external crises creating coordination demands, this one is entirely within your control.

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Enhance your leaders’ skill at building organizational alignment with a customized learning journey using our research-based modules. Available leadership topics include Boundary Spanning, Communication, the DAC Framework for Effective Leadership, Psychological Safety, Team Effectiveness, Thinking & Acting Strategically, and more.