An even fatter Homer (who looks like Homer when he gained weight to get out of going to work at the nuclear plant in King-Size Homer)
This is the third and final Treehouse of Horror episode that does not have the credits littered with "scary names" (the previous two were I and XII, the 1st one was because the specials were just starting, and the 12th one was because the writers felt that putting in scary names due to the 9/11 attacks was way too tasteless). This may have prompted some complaints from longtime fans, as the scary names were reinstated the following year.
This is the first Halloween episode to have the name Treehouse of Horror.
This episode is titled "Treehouse of Horror 13" as opposed to "Treehouse of Horror XIII".
The Island of Dr. Hibbert is parody The Island of Dr. Moreau.
As an owl, Lisa is no longer a vegetarian.
A deleted scene features Homer (as a walrus) gives Marge (as a panther) a back scratch she coughs up a hair ball and Dr. Hibbert plans on changing the whole animals back into humans.
In the second segment, when the first Homer goes to the past, we would have seen Homer already since the future is not altered until someone from the future goes back and alters it.
The War Room in this episode is very similar to the one seen in the Stanley Kubrick film Dr. Strangelove (Also seen in "Sideshow Bob's Last Gleaming") and one of the people in the room looks like George C. Scott who played General Buck Turgidson in the film.
In the Send in the Clones segment, when Marge comes back from shopping with a clone of Homer, as this occurs, the top part of one of the arch windows is missing.
When Homer is pulled into the back room by Prof. Frink, the piano music continues even though Homer isn't at the piano playing anymore.
When Patty and Selma are shown shooting a grave, the colors of their dresses are incorrect; Patty usually wears red and Selma usually wears blue.