The Sheegoth is supposed to be invulnerable to energy weapons, yet the bombs can hurt it.
Suit sounds should not be muted while underwater, since there is no water inside the suit itself.
Samus' suit protects her from the cold of space. If it can do this, ice attacks shouldn't affect her.
Samus' suit can protect against radiation, yet the X-Ray visor can see her forearm through the suit.
Zebes and Tallon IV are shown to be in the same system on a map, although they aren't.
The Artifact of Truth is out in the open despite the Space Pirates having looked for it.