The aim of this study is to explore how students experience and describe socio-cognitive and socio-emotional challenges in collaborative learning. The participants (N = 20) were teacher education students whose collaborative learning was supported with a designed regulation macro script during a six-week mathematics course. The purpose of the script was to provide structured phases during the collaborative learning tasks for the group members to plan, monitor, and evaluate their workings. The video data of groups' face-to-face work was collected and analysed by focusing on the different types of challenges the groups experienced and the types of challenges they described during the scripted interaction. The results indicate that the groups experienced more socio-cognitive challenges than socio-emotional challenges. The script provided them a moment to verbalize their emotional experiences, name the emotions (i.e. frustration), and attribute the challenges and emotions more precisely than during their mathematical task. The intertwining characteristics of socio-cognitive and socio-emotional challenges were observable. Collaborative learning can be challenging for groups, and thus, the knowledge of and the ability to implement practices for becoming aware of challenges can provide a direction for students to progress towards more productive collaboration.