Nice that you recommended a book of counterexamples. Counterexample books are particularly interesting for challenging your mental models. I picked one up when I took a measure theoretic probability class, and as I skimmed through the book I realized that much of what I thought was true (usually, implicitly) was not. (Can't think of any examples off hand, but this was the impression I had.)

Books of counterexamples and paradoxes are unfortunately not popular outside of math. In my own field, fluid dynamics, there's Hydrodynamics by Garrett Birkhoff, but nothing else I am aware of. In the first edition there was a discussion of D'Alembert's paradox that made me rethink a lot of what I had been taught about drag. This came down to understanding under what conditions the "paradox" holds, and recognizing these conditions are stricter than I had thought.