Chemical processes can be fully explained only by employing quantum mechanical models. These models are abstract and require navigation of a variety of cognitively taxing representations. Published research about how students use quantum mechanical models at the upper-division level is sparse. Through a mixed-methods study involving think-aloud interviews, a novel rating task, and an existing concept inventory, our work aims to fill this gap in the literature and begin the process of characterizing learning of quantum chemistry in upper-division courses. The major findings are that upper-division students tend to conflate models and model components. Students, unlike experts, focus on surface features. Our data indicates two specific surface features: lexical features and a "complex equals better" heuristic. Finally, there is no correlation in our data between a student's facility with navigating models and their conceptual understanding of quantum chemistry as a whole. We analyze the data through the lens of a framework which enables us to cast model conflation as a problem of ontology.