Collaborative problem solving is a core ability that has been highly valued in recent years. Collaborative problem solving activities allow learners develop collaboration skills. In science education, collaborative learning with simulations enables learners to manipulate a science problem to explore scientific concepts. However, the collaboration during such a learning context is a complicated process and researchers face difficulties in understanding learners’ mental effort in using the simulations. The use of dual eye-tracking techniques is helpful to uncover learners’ visual attention, and thus to better analyze student collaboration in activities. In this paper, the research focus on learners’ difficulties when they learn together with the simulation in different places. The results show that the techniques are helpful to identify the subtle interaction problem including the problem of lacking coordination, the process misunderstanding problem, and misunderstanding in partners’ attention. Educators may need to address these problems when simulations are applied to support remote collaborative science learning.