When Ganondorf is knocked off his horse in the final battle, he is seen holding his sword. But when he starts to get up, he has his sword sheathed.
In the flashback scene where Princess Zelda is offered the ultimatum to surrender or die, there is a close-up shot of her dropping her sword to the floor in front of her. In the overhead shot immediately following, Zelda is holding her sword again.
Any time Link is using the magnetic boots to walk on the ceiling, his clothes remain the same as if he was standing on the ground, that is, gravity does not seem to affect them. The only exception to this is in the Death Mountain dungeon, when Link is being carried by the magnetic cranes, when his hat does hang down.
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 two rotors.
One of the fans in Sky City does not have pitched blades, and therefore shouldn't be able to blow air.
Link's house does not have a bed even though it is implied he sleeps there at night.