It certainly does apply: why do men have nipples? Likely for reasons similar to why we have an appendix.
Fundamentally, natural selection and evolution are models that help explain general biological processes, to help us comprehend a bigger picture. Around the edges of that picture, it's not fully clear.
The truth is that the universe is governed by laws that are deeply unintuitive: general relativity and the standard model. Each layer of abstraction on these makes the periphery of the image fuzzier, but allows us to make more sense of the part of the image that we're focusing in on.
The same logic would apply to male nipples. It's a flawed logic.