Scientists say that, but they don't actually use the word "theory" that way, because they never bothered to make up another word that takes the place of "theory" when a theory bites the dust. So we still have luminiferous aether theory, the steady state theory, and caloric theory. In theory, we shouldn't still call them theories, but in fact we do.
Science is taught poorly, EVERYWHERE and that's why there are is so much confusion about terms. Part of the problem is that scientist themselves don't know how to use the term. I've read more than one medical article that use the word "theorize" rather than hypothesize. The other problem as you stated that there are many bad and outdated theories that poison the well.
Some people also get confused about a scientific law, as if a law can't be violated, but Bode's law of planetary distances is a good counterexample.
A scientific law is a theory in mathematical form. That's it but I've read so many text book and many refuse to explain it so clearly.