There are five unused icons in the game's files that might be from characters that went unused in the final game. They include Mandark, Wilt, Gwen, Schnitzel, and Captain Sticky Beard from Dexter's Laboratory, Foster's Home For Imaginary Friends, Ben 10, Chowder, and Codename: Kids Next Door, respectively. All of these characters (aside from Wilt) appear as assists in the game.

In Cartoon Network: Punch Time Explosion, each character's "Color 4" has pitch black skin, red eyes, and various other red and white elements, used by certain characters as their brainwashed selves in the story mode. Father, who was introduced to the playable roster in the XL iteration of the game, is already pitch-black, so his Color 4 makes him pitch-white, whereas fellow XL character Aku retains the pitch-black skin in his original design, but with red lips and white facial hair.