Toad puts on sunglasses when he decides to relax. In the next shot after Luigi grabs Toad, his sunglasses are gone. We don't see Toad remove his sunglasses.
When Mario is in the hallway with the Koopa kids on the wall in what appear to be "pictures" of them, their images change in the next shot,
When Koopa has the princess and Mario in the dungeon, the patterns of the bars on the cell door change between shots.
In one shot, when Koopa is leaving the Dungeon after the Princess is out of the cell, Cheatsy face turns the same green color as his head.
When Luigi and Toad are swimming underwater to enter Koopa's castle, there's one shot when Luigi's pants are red instead of green.
In one shot, when Koopa and Cheatsy are standing outside the cell that Mario and the Princess were in, Cheatsy's head turns brown.
In one shot during the beginning, Kootie Pie's whole face is brown.
When Cheatsy and Koopa are arguing over who gets the throne, the color on Cheatsy's face keeps changing color as he moves.
When Toad is complaining before he and Luigi dive underwater, Toad's lips aren't moving.