Every time I read something on quantum theory I can't help but notice how close to notion of magic it feels like. And I've studied physics in college. Some time ago I thought how strange these all would look to someone who had no knowledge in physics at all. But then I got it: two particles in different galaxies being entangled is not much different from calling someone on the other side of the globe using a cellphon…
I see it as a failure of the model. When the explanation is irrational, does a scientist stop to wonder at the irrationality of the universe instead of trying to come up with better explanations?
And what is more important - it's very hard to judge if the explanation is rational. Every science is built on some axioms which define what is rational and what is not. That's why I guess the progress happens step by step (each next step expanding what one would consider rational).