Continuity mistake: When Homer gets thrown out of the house by Marge and Otto walks up to him, you can see that it is Smithers and Carl standing behind Homer. Yet in the next shot when you see Homer's face, it is now Principal Skinner and Carl standing there.
Continuity mistake: The man conducting the tour of the box factory tells the children that they will not be able to see a finished box, as the boxes are assembled in a separate location. However, moments earlier we saw a flat box going through a machine, and coming out finished.
Continuity mistake: When the person delivers the animation cell, his skin changes from white, to brown and then back to white. When Bart looks through the letterbox to see who was there, his skin is white. When he gives the box to Bart, it is brown. When he hits Bart in the face and says "that's for keeping me waiting", it is white again.
Continuity mistake: When Marge comes home after the bogeyman incident, Homer trips over a footrest. You can see Bart sitting there however his pyjama's are a dark green color when before they were a bright green color. (00:16:35)