Following the 2024 Splatoon 3 world championships, Nintendo released a commemorative Splashtag banner depicting the winning team, Jackpot. However, shortly afterwards, the team became embroiled in controversy following allegations of racist comments and behavior both in and out of the game. Nintendo subsequently issued a statement on Twitter announcing that Jackpot's victory would be rescinded and that their banner would be redesigned due to them violating the game's community guidelines. Consequently, the Version 9.0.0 update replaced the design with a placeholder one depicting generic Inklings and Octolings. Nintendo additionally removed footage and social media posts of the championship from their website and social media accounts and pulled the Nintendo Switch News article announcing Jackpot's win.

The boss fight against Big Man in the single-player campaign appears to be an homage to Super Mario Sunshine's boss fight against the Phantamanta, with Big Man's ink being extremely similar in pattern and color scheme to the Phantamanta's goop, the method of attacking Big Man being splitting his shadow into smaller versions, and the boss title "The Hype Manta Storm" being a nod to the title of the mission in which Phantamanta is fought "The Manta Storm".

In the Side Order DLC expansion, the noises made by the bosses Asynchronous Rondo and Pinging Marciale are actually distorted clips of the Off the Hook songs "Ebb & Flow" and "Fly Octo Fly" respectively.