Contribution: This paper analyzes reflective thinking within organizational structures in higher education and draws parallels between the challenges faced by educators developing interdisciplinary courses and their students working in ill-structured projects. Background: Interdisciplinarity as a learning goal is prevalent across engineering education literature. However, without organizational support structures to guide faculty members in developing interdisciplinary courses, interdisciplinarity as a student learning outcome is difficult to sustain. There is a need to evolve existing organizational structures faculty navigate when creating interdisciplinary courses, so that competing organizational systems do not stifle interdisciplinarity. Moreover, educators' effort in developing interdisciplinary courses is mirrored in the uncertain processes in which instructors engage students. Research Questions: In settings of interdisciplinary curriculum design and implementation, how do interdisciplinary faculty collaborations parallel that of their student design teams? How do organizational structures affect interdisciplinary faculty teams designing courses that span disciplines? Methodology: The study used a qualitative case, bound by three required courses in a new interdisciplinary undergraduate minor. Data was collected via interviews, class observations, and student reflection assignments. Analysis was guided by the conceptual frameworks of King and Kitchener's reflective judgment model and strange and banning's conceptualization of campus learning environments. Findings: Both educators and students develop through the discomfort with uncertainty--a prevalent theme in complex problem-solving. Forms of summative assessment pose an added challenge for both groups as they negotiate organizational structures. Lastly, discipline-specific expectations and ways of valuing knowledge contribute to uncertainty through the interactions among groups.