Complex systems are typically difficult for students to understand and computer simulations offer a promising way forward. However, integrating such simulations into conventional classes presents numerous challenges. Framed within an educational design research, we studied the use of an in-house built simulation of the coagulation network in four pharmacy undergraduate classes. Drawing upon audio recordings of small group discussions, focus group interviews, and class observations, we identified implementation challenges related to: adaptation of simulation to align with student needs; compromises to learning design; and classroom infrastructure. These findings can serve to guide teachers and staff developers on the common challenges that are likely to arise from integrating computer simulations meaningfully into realistic contexts. (Contains 3 figures and 1 table.)