Atoms of confusion are small patterns of code that have been empirically validated to be difficult to hand-evaluate by programmers. Previous research focused on defining and quantifying this phenomenon, but not on explaining or critiquing it. In this work, we address core omissions to the body of work on atoms of confusion, focusing on the 'how' and 'why' of programmer misunderstanding. We performed a think-aloud study in which we observed programmers, both professionals and students, as they hand-evaluated confusing code. We performed a qualitative analysis of the data and found several surprising results, which explain previous results, outline avenues of further research, and suggest improvements of the research methodology. A notable observation is that correct hand-evaluations do not imply understanding, and incorrect evaluations not misunderstanding. We believe this and other observations may be used to improve future studies and models of program comprehension. We argue that thinking of confusion as an atomic construct may pose challenges to formulating new candidates for atoms of confusion. Ultimately, we question whether hand-evaluation correctness is, itself, a sufficient instrument to study program comprehension.