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As part of a larger case study on the capstone course of a teacher education program, the end of semester reflections of preservice STEM teachers are analyzed. Patterns in the perceived failures while engaged in classroom teaching are discussed. These patterns are further investigated through four reflections from preservice biology teachers. Findings demonstrate that preservice STEM teachers focus heavily on pedagogy and classroom management when reflecting on challenges in classroom teaching. Our analysis shows that responsive, guided reflection driven by the teacher educators’ perceived themes within preservice teacher reflections helps preservice teachers to build stronger understandings of the challenges of teaching and make better use of reflective activities to plan for future lessons.