After Scrapper drops the cauldron of water, it vanishes.
Fi never calls Link by his name; instead it is entirely different.
Some objects fly using a single rotor to stay aloft. Nothing can fly with less than 2 rotors.
The method of turn windmills so that they always face the wind wouldn't work because the pinwheel is on the back.
There should not be sinksand aboard the ship's upper levels.
It is never explained how Zelda makes it to areas that Link has to solve puzzles and open doors to get to.