Discipline-based science concept assessments are powerful tools to measure learners' disciplinary core ideas. Among many such assessments, the Brief Electricity and Magnetism Assessment (BEMA) has been broadly used to gauge student conceptions of key electricity and magnetism (E&M) topics in college-level introductory physics courses. Differing from typical concept inventories that focus only on one topic of a subject area, BEMA covers a broad range of topics in the electromagnetism domain. In spite of this fact, prior studies exclusively used a single aggregate score to represent individual students' overall understanding of E&M without explicating the construct of this assessment. Additionally, BEMA has been used to compare traditional physics courses with a reformed course entitled Matter and Interactions (M&I). While prior findings were in favor of M&I, no empirical evidence was sought to rule out possible differential functioning of BEMA that may have inadvertently advantaged M&I students. In this study, we used Rasch analysis to seek two missing pieces regarding the construct and differential functioning of BEMA. Results suggest that although BEMA items generally can function together to measure the same construct of application and analysis of E&M concepts, several items may need further revision. Additionally, items that demonstrate differential functioning for the two courses are detected. Issues such as item contextual features and student familiarity with question settings may underlie these findings. This study highlights often overlooked threats in science concept assessments and provides an exemplar for using evidence-based reasoning to make valid inferences and arguments.