When Bart and Millhouse are playing on the "Wacky Shack" in one of the factory scenes, Millhouse points out to Bart the warning signs on it. There are three, but Bart only removes two and throws them out of a nearby window. When we see the shack again a few seconds later, all three signs have gone.
The hole Frank Grimes makes in the wall with the acid keeps changing shape, bigger than the still-crumbling drywall can account for. For example, when it's first made, there is a much smaller hole in one corner that disappears completely.
During his nervous breakdown, Grimey imitates Homer saying "D'oh! D'oh! D'oh!", even though he never once heard Homer say his catchphrase.