Computer-supported collaborative learning (CSCL) environments may at times become socio-emotionally tense and pose challenges that may have detrimental effects on mutual trust and shared mental models. Objective: This study aims to examine and classify general teamwork challenges in a novel but authentic CSCL setting (hackathon) to identify challenges that impede the development of key team coordination mechanisms (i.e., mutual trust and shared mental models). Methods: Multimodal data including responses to an adapted questionnaire (AIRE), post-competition interview data, and videos of team interaction were collected during an international hackathon event (N = 48, 71% male, M = 22 years age). Qualitative theory-driven coding and theme development were used to analyze the multimodal dataset (Greeno, 2006; Jarvenoja et al., 2013). Results: Our analyses revealed 16 general challenges that hamper teamwork in a hackathon. A model of team challenges was developed to categorize challenges into macro level themes including cognitive, motivational, emotional and behavioral challenges. We also identified which challenges hindered the development of mutual trust, and which challenges hindered the development of shared mental models. Conclusions: These findings provide important insights for educators and mentors in understanding the types of teamwork challenges that may occur in CSCL settings. The results also inform educators which challenges likely lead to mutual trust breakdown and weaken shared mental model bonds.