After Scrapper drops the cauldron of water, it vanishes.
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.
Fi never calls Link by his name; instead it is entirely different.
There should not be sinksand aboard the ship's upper levels.
Despite this game being the first ever game in the Zelda time line chronologically, the technology is the most advanced the series has ever gotten, having functioning electrical lights, robots, enemies with electrical weapons, and so on.
It is never explained how Zelda makes it to areas that Link has to solve puzzles and open doors to get to.