When Rodney and Fender are pulling the lever, the rooms are located one above the other (i.e., arranged vertically). But during the "armpit farts" sequence, the light in Piper's room is to the left of the building, while Crank's is to the right.
When Wonder-Bot puts the second group of dishes into Rodney's father, they are facing to the right. When he takes them out, they are facing to the left.
After surfing the waves of dominoes, Bigweld flies up into the air, and then lands. When he flies up, you can see dominoes fly up with him. But when he lands, no dominoes fall down after him.
When Rodney uses Wonder-bot to help his father wash dishes in the kitchen at the diner, his dad has 3 dirty plates already in his "stomach dishwasher". Wonder-bot adds 6 more plates, bringing the total of dirty plates inside dad to 9. Seconds later when Wonder-bot takes the newly cleaned plates out of dad's "stomach", there are only the 6 that were added. The original three are missing.
Just before Rodney takes the city ball express, you can see him standing on a giant cog turning downwards. In the wide shot, the cog above him clearly has a robot on it too, yet when Rodney hops off, the cog above him comes down, and there is no robot to be seen.
After Rodney accidentally starts the dominoes in Bigwelds office, during Bigwelds surf, Rodney and Cappy are just floating waist up in the big wave of dominoes and stay upright without moving their arms, completely defying the laws pf physics.
Before Bigwell came to confront Ratchet at the end of the movie, Cappy was wearing her black high-heeled shoes, but when she appeared after this scene, her shoes are gone for the rest of the film for an unknown reason.