Molecular orbital diagrams are commonly taught and used for describing chemical bonding chemistry courses including courses at the college level. Misconceptions that occur when students construct and/or use these diagrams are difficult to anticipate, diminish the diagram utility, and limit student learning. In this exploratory study, a combination of think-aloud activities and written probes was used to identify misconceptions that persist into upper-level college chemistry courses. While the majority of students could properly construct molecular orbital diagrams, many struggled to use and interpret the resulting diagrams. Pronounced disconnects between the depiction of chemical bonds and how these depictions demonstrate molecular properties such as stability and reactivity were observed, informing strategic curricular interventions.