When ghosts are turning back into paintings at the end of an area, a picture of three ghosts playing cards is shown on a screen on the machine. These ghosts are actually from a one second clip for Luigi's Mansion from the GameCube reel at Spaceworld 2000.

Using an Action Replay code, it's possible to actually walk around E. Gadd's lab. There are two doors, one of which says "Training" that most likely went to the Training room, and one that likely went to the Ghost Portrificationizer room. There is also a functional ladder, but it doesn't lead anywhere. This suggests that in an earlier version of the game the player could travel to E.Gadd's lab by means of a ladder somewhere in the mansion.

In earlier versions of Luigi's Mansion there was a timer on the HUD. According to Nintendo Power Magazine, this was because Luigi had only 24 hours to save Mario. It was never explained what happened if he failed, but fans have speculated that Mario, along with the Mansion, would have disappeared, or that Luigi would have been possessed. This speculation is based on leftover 'Ranking' files in the game's data. Three unused renders show Luigi holding a flower and looking depressed, him looking happy and making a peace sign, and another of him making two peace signs.

Before going into the Training Room in the original game, a menu will appear giving the player different controller options. After waiting for a couple of minutes, the music track will change to a funky beat, 19 notes will play, and the original music will then return. These 19 notes are actually Totaka's Song, a song that is hidden in almost every game composer Kazumi Totaka has worked on. In the game's Nintendo 3DS remake, this control selection screen only appears during the first time you go to the Training Room, giving you only one chance on that save file to find this Easter egg.

On the file select screen, a message will appear and disappear that says, "Welcome to your mansion." However, the "y" in "your" fades away a split second before the rest of the message, so that it reads, "Welcome to our mansion." The copy and erase messages are also spooky: when choosing a file to copy, the message says, "More files means more fear." Selecting erase causes the message to alternate between "You can erase the files" and "but not the fear."

Luigi's Mansion was originally developed with the intention of being in 3D. All Nintendo GameCube systems support display of stereoscopic 3D. Nintendo decided to shift focus away from 3D at the time as a 3D screen add-on would have cost more than the Gamecube system itself. Stereoscopic 3D would later be used in the game's Nintendo 3DS remake.

If Luigi confronts King Boo before capturing all of the portrait ghosts, he will say "I will not give up my favorite decoration, I like Mario just where he is." This is a reference to Star Wars Episode VI: Return of the Jedi. When Han Solo is trapped in carbonite, Jabba the Hutt says: "I will not give up my favorite decoration. I like captain Solo where he is." Both Mario and Solo being sealed away seems to reinforce this connection.

The October 2001 issue of Nintendo Power included a page with preview screenshots of Luigi's Mansion, including a screenshot of an earlier build of the Safari Room with the caption: "When your ghoul-busting mission takes you to the trophy room, proceed with caution. If you meet up with the ghost of a hunter, he'll want to add Luigi to his collection." This sparked rumors among players that the Safari Room originally featured a hunter boss who wanted Luigi's head as one of his trophies, and that it was removed from the game for being too frightening to the target audience of children.

However, no evidence of a hunter ghost is present in the game's data despite the presence of other unused ghosts, and no direct mentions of the boss exist in previews prior to the game's release in Japan in September 2001. The caption was likely an attempt at hyperbole rather than a serious indication that a hunter-themed ghost was in the game, as the article was written after Luigi's Mansion was released in Japan, meaning all characters would have been finalized long before the article was published.