Rocko from Rocko's Modern Life was intended to appear as a playable character in Nicktoons MLB but was scrapped for unknown reasons, with the only remnants of his appearance being his skeleton and a small black square labeled as his texture. Rocko's Modern Life is the only Nickelodeon show without a playable character to be referenced in the opening copyright credits.

Nicktoons MLB's loading screens include cameos from a variety of Nicktoons characters, including those from cartoons not featured on the playable roster. One of these characters is George Liquor from The Ren & Stimpy Show, a character that series creator John Kricfalusi retained the rights to after being fired from the series, and would use in a variety of cartoons up until his blacklisting from the animation industry in 2019. Since Kricfalusi is not credited in the game's copyright screen (though he is still listed in the special thanks credits alongside all other show creators), it seems that Liquor was included by mistake.