Adding caches or switching to lower-level calls is definitely something learned, and I wouldn't call it "intuitive".
What I think you are referring to is that sometimes, simply reading and understanding the code can tell you where the problem really is — still, my experience is that you want to measure the before and after to at least identify the general area you should be looking at, and more often than not, I could figure out what needs optimizing and how without having to get detailed profiles.
I did end up being surprised a few times, but it was mostly due to external code like buggy library implementations that didn't do the things they promised (eg. async library really synchronizing everything with a badly placed mutex).
At the same time, it's wrong to focus on a single case or a single profile (executing one code path in one set of circumstances), but what you are describing simply sounds like bad engineering — the fact that you can misuse the tool does not make the tool bad, it's still the engineer wielding it who's at fault.