The large house that Link travels to in the mountains has a bedroom on the third floor. This bedroom is only accessible from outside, which, considering the climate, does not make sense.
Some enemies fly using a single rotor-like appendage. It is impossible to fly with anything less than 2 rotors.
One of the fans in Sky City does not have pitched blades, and therefore shouldn't be able to blow air.
Ilia remembers that she was being held captive in the Hidden Village, before escaping to Hyrule Castle Town. The Gorons, however, remark that the village has been inaccessible for a long time due to a rockslide. It is never explained how Ilia was able to get in and out of the village, if it is supposed to be completely sealed off.