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Developing collaborative skills in students is nontrivial. The fact that students work in teams does not mean they become skilled in teamwork. Students face varied challenges when working in teams that harm their skill development and attitude towards teamwork. To prepare students for the collaboration-intensive workplace, we researched and designed a catalog of challenges present in the teamwork of undergraduate software engineering students on 3-month projects. We created an initial catalog of 10 challenges by examining the literature, surveying 15 teaching assistants, and coding their opinions regarding the problems faced by student teams. Using the catalog, we crafted a survey for students nearing the end of their team project to assess which challenges were present in their teamwork. We surveyed students from multiple contexts, including teams of 3, teams of 4, and teams of16 students. We analyzed 155 answers to determine the prevalence and intensity of the 10 challenges in student teams. We discuss our findings and best practices for resolving the most prevalent challenges. The catalog and recommendations are directly valuable for software engineering educators and can inform the broader community of collaborative learning researchers and instructional designers. © 2023 MIPRO Croatian Society.