According to producer Chuck Beaver, all of the game's FMV cutscenes were originally planned to be made in 3D using the in-game models. Late in development, Fox requested that they be changed to 2D animation in the style of the TV show, as they felt the 3D-to-2D approach didn't produce results that were "on-model". These 3D cutscenes still appear in the Nintendo DS version, though with some scenes, music, and sound effects removed, likely because they were unfinished.

Several level names were originally different during development:

• Lisa the Treehugger was originally called The Treehugger.
• Enter the Cheatrix was originally called Cheater, Cheater, Pumpkin Eater.
• Invasion of the Yokel-Snatchers was originally called The Day Springfield Stood Still.
• Five Characters in Search of an Author was originally called Rhymes with "Complaining".
• Game Over was originally called Meet Thy Player.

Despite the changes, the original names still remain in the game's code and file structure. Many of these early titles appear in early builds, and "Cheater Cheater" and "The Day Springfield Stood Still" were even reused for song names in the game's official soundtrack.

The New-Gen E3 2007 build of the Xbox 360 release revealed that the home console versions were originally meant to have cutscenes fully animated in 3D. A workprint containing these cutscenes shows a mix of finished and unfinished 3D renders and storyboards with placeholder voice acting, with the final game having cutscenes primarily animated in the same 2D digital animation as the show. The Nintendo DS version of the game is the only version that exclusively uses 3D cutscenes.

This build also reveals that the identity of the "sleazy video game producer" featured in Level 5: Mob Rules is Larry Probst, the former CEO of Electronic Arts from 1991-2007. The name is not fully censored in the DS version of the game, where Marge can be heard faintly saying his name under the censor tone in the level's opening cutscene. Probst's name also appears uncensored in the in-game cutscene for the level, where the dialogue is fully intact. In the final retail versions, the name is censored from the game's script when Mayor Quimby says it.

The game manual featured throughout every version's cutscenes (except the DS version) is the cover from the Xbox 360 version. The DS version, however, is actually from the in-game cutscenes used from every other version. Interestingly, the DS version’s cutscenes resemble the in-game ones from the other versions.

All "in-game" cutscenes from the Xbox 360 and PlayStation 3 versions were imported to the PlayStation Portable, Wii, and PlayStation 2 versions of the game despite obvious inconsistencies with the level designs.

Unused victory fanfares for each stage can be found in the DS version's data. In the final game, the main menu theme replaces these.