Two-tiered assessment structures with paired content and confidence items are frequently used within chemistry assessments to stimulate and measure students' metacognition. The confidence judgment is designed to promote students' reflection on their application of content knowledge and can be characterized as calibrated or miscalibrated based on their accuracy. Previous studies often attributed students' miscalibrated confidence rankings to metaignorance, however, in this qualitative study, interviews with general chemistry students were thematically analysed to provide a more robust understanding of the processes and factors students use when engaging with these metacognitive prompts in a chemistry assessment. Both calibrated and miscalibrated confidence judgments were observed independent of accuracy. Students who provided miscalibrated confidence judgments often used unreliable metrics such as processing fluency which can mimic content mastery whereas students who provided more accurate evaluations of their confidence relied more heavily on their stable understanding of chemistry concepts. Many students cited previous experiences, underlying self-efficacy beliefs, and/or the use of test-taking strategies which negatively or positively impacted their confidence. These findings suggest that the confidence tier is indeed capturing students' self-assessment, however, students' confidence judgments are based on a range of factors independent of content knowledge which may impede on the utility of this metacognitive tool for students, researchers, and instructors.