When students experience confusion, resolving that confusion can lead to deeper understanding and engagement. Persistent unresolved confusion, however, can lead students to frustration and disengagement. Our research explores confusion and other emotions associated with learning as students work through elicit confront resolve (ECR) activities in Next Generation Physical Science and Everyday Thinking (Next Gen PET) physics courses for future elementary teachers. We used the experience sampling method (ESM) to measure students' subjective experiences during seven particularly confusing activities. The ESM asked about confusion, self-efficacy, engagement, and stress, which we chose to align with existing models of confusion in learning. After some revision, our model fit the data well using confirmatory factor analysis. The only activity that required students' consistent use of mathematics produced the highest levels of confusion and stress for students. This relationship with mathematics content indicates the Next Gen PET courses could better support future elementary teachers developing fluency and comfort with mathematics.