When Mario and Luigi steal a police car and are being chased, as they enter the tunnel there is a message on the computer screen that says "WARNING: TUNNEL NOT FINNISHED", which contains a spelling mistake.
When the Bob-omb blows up under Koopa's legs, he flies into the air, and is shown shortly after falling straight down. But in the shot just after, he falls at an almost 45 degree angle into the suspended bucket.
When the van breaks down at the beginning of the film, it has some lengths of piping strapped on the side and overhanging out a couple of feet at the back. Once the van has stopped, the copper piping is nowhere to be seen.
As the camera pans back from normal Toad sitting in the Devolution Chamber chair, you can see Simon and a worker with a red helmet to the far right. The first time you see the worker, he is played by a heavier set man. In the rest of the scene he is a different and skinnier actor.
When Mario and missing Brooklyn girl exit the frozen vent on mattress they fly through the air, after reaching the floor the slide for a few moments, a mattress would not slide with the weight on it, the would simply be thrown off.