Hugh Neutron has a secret command input move based on Chun Li's Hoyokusen from Street Fighter III: 3rd Strike, which can be activated by doing a 360 input then pressing taunt.

In the release version of Nickelodeon All-Star Brawl, the stage Royal Woods Cemetery from The Loud House contained a hazard where tombstones would pop out of the ground, sending any character beneath them flying and remaining as a wall for a short while afterwards. In version 1.5.0, the update that added Rocko as a playable character, this hazard was removed from the game completely, making the stage into a flat floor, similar to Final Destination from the Super Smash Bros. series. The reasoning for this change is because the stage that was intended to serve as a Final Destination parallel, Harmonic Convergence from The Legend of Korra, was considered too long for use in competitive play, and was removed from this distinction in the same update.

At one point in the game's development, SpongeBob's strong dash attack was intended to involve him running with scissors. This was vetoed by Nickelodeon, with community manager Thaddeus Crews suggesting that Nickelodeon may not have wanted a character many children view as a role model partaking in an easily-imitable dangerous activity. The scissors exist in the game files, attached to SpongeBob's model, but in an untextured form with no bones for snipping.

In the final game, SpongeBob's strong dash attack was a slip and fall based on a single frame from the episode "Krabs à la Mode" that became a meme.

An early title screen in the game data suggests the game's original title was "Nickelodeon All-Star Brawl Universe". For unknown reasons, the "Universe" part was dropped.

Previews for new fighters being added to the game showed that one of Jenny's intended pre-battle quotes was "You wouldn't like my brain! It's all circuity and metallic!" While this line was taken from an episode of My Life as a Teenage Robot, it was removed from the final game due to it being associated with a pornographic parody of that episode by Internet animator Zone, which edited the line to replace "brain" with "body."

Thaddeus Crews, a member of the development team and community manager, initially expressed disgust in a now-deleted tweet (the tweet he replied to also having been deleted) that the line was in the game and announced its immediate removal. He later explained that the line was likely added due to a lack of awareness about the parody, the end result of the team being "spread out and not on the same page", while adding that "Most likely someone on the team did know what they were doing by adding it", despite Crews himself being previously aware of and publicly associating the original line with the porn parody prior to its removal from the game.