Learning to interpret organic structures not as an arrangement of lines and letters but, rather, as a representation of chemical entities is a challenge in organic chemistry. To successfully deal with the variety of molecules or mechanistic representations, a learner needs to understand how a representation depicts domain-specific information. Various studies that focused on representational competence have already investigated how learners relate a representation to its corresponding concept. However, aside from a basic connectional representational understanding, the ability to infer a comparable reactivity from multiple different functional groups in large molecules is important for undergraduate students in organic chemistry. In this quantitative study, we aimed at exploring how to assess undergraduate students' ability to distinguish between conceptually relevant similarities and distracting surface similarities among representations. The instrument consisted of multiple-choice items in four concept categories that are generally used to estimate the reactivity in substitution reactions. This exploratory study shows that the item design for assessing students' conceptual understanding influences students' answering patterns. Insights and pitfalls gained from this investigation and future directions for research and teaching are provided.