The Energy and Momentum Conceptual Survey (EMCS) is a multiple-choice survey that contains a variety of energy and momentum concepts at the level of introductory physics used to help inform instructors of student mastery of those concepts. Prior studies suggest that many concepts on the survey are challenging for introductory physics students and the average student scores after traditional instruction are low. The research presented here uses the EMCS to investigate the extent to which upper-level students have developed mastery of energy and momentum concepts both before and after an upper-level classical mechanics course. To contextualize their performance, it will be presented alongside the performance of introductory students. Additionally, a different set of upper-level students provided explanations for their answers to each question, and those explanations were useful for understanding their common difficulties with energy and momentum concepts. We discuss some of the most challenging questions on the EMCS for upper-level students and common reasons they had difficulty with those questions.