When thinking about measurement uncertainty in a laboratory experiment that features quantum mechanical effects, it is important to consider both the physical principles of underlying quantum theory (e.g., the uncertainty due to quantum mechanical superposition states) as well as the limitations of the measurement (e.g., the spread in outcomes due to instrumental imperfections). Prior research has found student difficulties with these sources of uncertainty both individually and in students' ability to distinguish between them. Additionally, students are less likely to access ideas related to experimental uncertainty in quantum mechanical contexts unless explicitly prompted. In this work, we have developed a simulation-homework activity focused on the Stern-Gerlach experiment to help students develop an understanding for the different ways that modifying the quantum state, improving the experimental setup, or collecting more data, will affect the resulting outcome distribution. The activity uses a purpose-built interactive simulation, coupled with homework questions grounded in the literature on student thinking about uncertainty. We analyze the effectiveness of the activity with students in junior-level undergraduate quantum mechanics courses using pre- and post-testing. The results indicate that the activity was successful in helping students distinguish between quantum mechanical uncertainty and uncertainty caused by instrumental imperfections, and in increasing the accessibility of instrumental limitations in this context. The activity can thus support student understanding of the core concept of quantum uncertainty, as well as link between the often abstract nature of quantum theory and laboratory experiments with their limitations.