Krusty's five-o-clock shadow is colored in dark pink.
When Marge wakes up by the leak, it is nighttime. However, when Homer fixes the leak with the Hot Wheels track, it is daytime.
As Lisa chases her hamster, the house has more doors than normal.
When Bart arrives at the entrance, it is not raining outside. But later, it is raining again.
Homer technically didn't spill the beans about Lenny's surprise.
When Homer sits on Lenny's bar stool cake, the outside cover is red. But later, it is light red.
Why would they place the cake on the floor without a plate under it? It would probably give away the fact it was a cake.
When Homer's painted portrait of an angry Marge is seen on the house, the living room's window is missing.
Homer's car is in a different shade of pink-purple in the Simpson house shot seen at the beginning of Act 2.
When Homer calls "Ray" to save him from the mental hospital's medical restraint, Dr. Hibbert's eyebrows are missing. Later, after Bart tells Homer that he only saw him talking to himself, Dr. Hibbert's eyebrows are colored in.
When the family (except Homer) arrive at the Calmwood Mental Hospital to check on Homer, there is no building in front of it. But when the Simpson family, Ned and Dr. Hibbert visit Homer in his patient room, the Flanders house is in front of it with Ray on the roof, as seen in the patient room window. The Flanders house might've been so far away from the mental hospital that the house can be seen from the hospital.
The Knockers bartender should have seen (or at least heard) Ray, as he ordered the giant cup of beer and the nachos before Homer sat with him. But, the bartender had an eyepatch covering his left eye, so he only saw Homer and not Homer with Ray in the first place.
The Knockers bartender was at the mental hospital along with the rest of the Simpsons, Dr. Hibbert, Ned and Ray when they came to see Homer after the six-week electric shock treatment. However, he disappears when Stephen Hawking appears.
When Stephen Hawking explains how Bart couldn't see Ray at Builders' Barn, the flashback does not show a ladder behind Ray. In the original scene, there was a ladder behind him.
The gravitational lens created by the black hole should have absorbed the light of other stuff that was near Ray and Homer.