Plot hole: After Mario and Luigi have defeated King Koopa, Daisy's father and the man in New York re-evolve back to their human forms. This makes no sense as it is never explained, and none of the goombas, koopas or troopas ever revert.

Continuity: In Devo 4 Luigi's button unbuttons and rebuttons itself.

Factual error: Mario says about his girlfriend "I promised to take her to Wrestlemania." The problem is that Wrestlemania took place in Las Vegas that year. The event took place in NYC's MSG the following year.

Continuity: In the scenes where the devo chamber is when Toad is devolved the Advance sign is black. When they evolve Spike the sign is red.

Factual error: 191 X 191 = 36481, not 26481.

Audio problem: When Mario and Luigi are in the cave, walking along the cliff, Mario shouts "Watch out" but his mouth never moves.

Continuity: 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.

Continuity: 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: The Mario Bros. appear briefly without their tool belts after they enter the alternate dimension.