The outside of buildings does not match the inside.
Some enemies use a single helicopter-like rotor to hover. Nothing can hover on rotors with less than 2 rotors.
The Strange Flute is in a horn shape and not a flute shape.
The town of Symmetry isn't symmetrical.
Maple can appear in any time despite having no apparent way to travel through time.
Link was told that the stone he 'blasted' near the Ancient Cave was holding up the cave, but Link lifted the stone; he did not blast it.