Continuity mistake: In the devo chamber, when Toad is devolved the Advance sign is black. When they evolve Spike the sign is red. (00:36:20 - 00:46:45)
Continuity mistake: The Mario Bros. appear briefly without their tool belts after they enter the alternate dimension. (00:23:05)
Continuity mistake: When Mario and Luigi are in the elevator with the Goombas they're still wearing their specialised jump boots. The instant they get out of the elevator they're back in their normal shoes. (01:06:30 - 01:10:50)
Continuity mistake: When Mario and Luigi follow Koopa's goons into the cave, Luigi jumps through the portal in the wall but Mario is more hesitant. When he falls toward it, in one shot his feet have barely left the ground, but in the next shot immediately afterwards he is pretty much upside down as he falls through the wall.
Continuity mistake: A Bob-Omb explodes under the devolving Koopa and sends him flying. The shot shows him flying straight up, and without cutting, shows him begin to fall along the same trajectory. The big pot thing is off to his left, and well out of reach of him falling. Yet then it cuts to him falling at an obvious angle and into the pot. The trajectory was all wrong.
Continuity mistake: Just after the car chase scene, Mario drives the police car into a tunnel, which disconnects the vehicle from the power grid. The car even says, power shutting down, causing the monitor to shut down, and for the breaks to stop working. However, even after the car leaves the tunnel and is dangling in fungus, way out of reach of the power, the headlights and the police lights of the car are still lit. They should have shut down also when power was lost.
Continuity mistake: When Toad is talking to Mario and Luigi in the jail cell, he has his arms dangling down through the grate into their cell. When the camera is looking up at Toad, his arms are sticking through grates that don't align with each other, but during overhead shots his arms are through grates in the same row.