Quantum mechanics is an example. We know how to use QM. It is an amazing theory. But physicists aren't probing QM anymore. Well most aren't. It does such a good job spitting out answers, we don't ask why. There is a lot to be explored there but academia tells people to avoid it. They say don't look at the man behind the curtain. QM is equations that gives good answers but we don't really know why.

Something Deeply Hidden is a good book on the subject(as a non physicist).

Of course I am just a layman who likes to read books about these subjects but I honestly don't know shit. Just what I read.