Revealing mistake: In the live-action segment, when the Super Plant chases Mario and Luigi, the actor's shoes can be seen. This also happens when the Super Plant heads over to Dr. Toby. (00:17:43 - 00:18:57)
Continuity mistake: After Mario drains the dungeon, Toadstool and Toad jump off the shackles they were hanging off. However, when Mario jumps off, Toad is again seen hanging from the shackles even though he had previously jumped down. The next scene confirms this by having him on the ground where he belongs. (00:10:28)