Yes they did, we just hadn't figured them out yet. If we were very wrong in them, we'd have to be wrong in a way that doesn't affect all the technology using the wrong theory - which is part of why we refined them, because shit didn't work.

That's what it means to be contradicting fundamental physics. It implies all of our other knowledge is wrong, but we are just lucky enough that our machines work anyway. Which, unless we see a phenomenon that we can't fit into our existing theories, seems unlikely