Confusion is an important epistemic emotion because it can help students focus their attention and effort when solving complex learning tasks. However, unresolved confusion can be detrimental because it may result in students' disengagement. This is especially concerning in simulation environments using discovery-based learning, which puts more of the onus for learning on the students. Thus, students with misconceptions may become confused. In this study, the possible moments of confusion in a simulation-based predict-observe-explain (POE) environment were investigated. Log-based interaction patterns of undergraduate students from a fully online course were analyzed. It was found that POE environments can offer a level of difficulty that potentially triggers some confusion, and a likely moment of students' confusion was the observe task. It was also found that confidence in prior knowledge is an important factor that can contribute to students' confusion. Students mostly struggled when they discovered a mismatch between the subjective and objective correctness of their responses. The effects of such a mismatch were more pronounced when confusion markers were analyzed than when students' learning outcomes were observed. These findings may guide future works to bridge the knowledge gaps that lead to confusion in POE environments.