Not so. They may have been conceptually impossible but did not run into the "fundamental" laws of physics. FTL travel breaks physics. A lot abiut our observable universe would be different if it were possible.
The evidence that the universe obeys these laws is significant and, currently, not counter indicated.
Those "fundamental" laws of physics didn't exist several centuries ago.
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
Like quantum mechanics broke physics?
So yes, perpetual motion could start working tomorrow, or could already exist for all we know. That doesn't mean it's wrong to say physics _currently_ says it's impossible and any claim better have some pretty good evidence to dispute it (which none currently do). But that also doesn't mean that if we're around centuries/millennia from now we won't have found a special case where our current understanding breaks down.
For all we know, our understanding of the universe could be at a stage of analogous to “there are four elements: earth, air, fire, and water”. Many things that we enjoy daily were once “fundamentally impossible”.