When Toad comes to break the news about a pair of Para Goombas coming to eat the kingdom for lunch, there's a shot where the princess has her hands on her face. In the next shot where Koopa is heard laughing, she puts her hands down. Then in the next shot, her hands are back on her face.
In one shot in the lab when Kookie and Cheatsy are making more "nice guy" potion, Cheatsy's face turns green.
When Cheatsy and Kookie are making another batch of "nice guy" potion, there are a few close ups of Kookie's arms being green when he's holding the potion.
When Koopa starts complaining about being nice, Cheatsy's face changes color from green to his skin color.
When Cheatsy and Kookie peek into the window at Mario and Luigi's house, the green on the top of Kookie's face vanishes for the shot, then reverts back to green in the next shot.