The existence of logic seems somewhat mysterious. It's this thing that seems to exist, but unlike other things that exist, it doesn't seem to exist anywhere in specific or in any tangible form. Further, while it is easy to mock Plato for mysticism when he posits perfect forms existing in some kind of mysterious Platonic Realm, that's actually uncomfortably close to a description of what logic is often seen as.
Appliability of logic in physical world is sort of a theorem based on the laws of physics (mostly more metaphysical and less technical like the persistence of objects, that themselves as theorems of the basic laws of physics) and the laws governing the process of formulating atomic statements based on the observations.
At the same time we need to be careful as we can easily fall into the trap of unfalsifiability -- when the predictions of logic fail, we're used to say that the problem was with our atomic statements.
That's just the sketch of the full explanation of the topic, which would require at least a chapter.