Toxicologic pathologists play a crucial role in the evaluation of animal studies for drugs, environmental chemicals, medical devices, and other agents to determine their safety and potential toxic effects. A significant challenge in this domain is the differentiation between incidental or procedural changes and genuine treatment-related effects. Correct identification and interpretation of such findings are essential to ensure that safety assessments are accurate and reliable for subsequent approval for human use. This review presents several cases in which non-test item-related findings were encountered. By examining procedure-related findings and considering spontaneous background pathology, we underscore the need for meticulous pathological evaluation and proper contextual understanding to avoid misinterpretations that could lead to erroneous conclusions about a substance’s safety profile. The insights shared in this review aim to enhance the proficiency of toxicologic pathologists in recognizing and managing various interpretative challenges, with the goal of ultimately improving the accuracy of toxicological assessments, thereby contributing to the safe development of new therapeutics and medical devices and sound characterization of potentially hazardous substances in our environment.