The spitting piranha plant that attacks Mario and Luigi when they are looking for Junior is green. Then the plant turns red when he's retreating.
When the Boomerang Brothers first see junior, they are orange. In the next shot when one of them throws a boomerang at Junior, they are both green. Then when Junior throws the boomerang at the tree, the Boomerang Brothers are orange again.
Outside the volcano when Kooky says it's time to "heat things up in the pipe maze," Bully's shell is green instead of pink.
After Mario forces Luigi through the hole when they are escaping from the lava, the lava reaches Mario's knees before he exits through the hole. The lava should of harmed him.
When the volcano is about to erupt, Junior gets hit in the face by a dirt clot from the volcano. In the shot when Luigi brushes the dirt off of Junior, Junior has nothing on his face until Luigi touches his head.