The game contains an unused enemy called "Scoot Bloop". Its sprite and attack animations are complete but its battle script seems to be unfinished.

In the North American version of Mario & Luigi: Partners in Time, the Elder Princess Shroob's crown is given an attack rating, although the crown never actually attacks, as its purpose is to simply protect the princess from damage. In the Japanese and European versions of the game, this has been corrected, with the crown having a Power rating of 0.

There is an unused Whomp character in the game's data. He has several animations, but doesn't appear anywhere in the game.