In late 2023, Garry's Mod creator Garry Newman received a copyright takedown notice from the film production company Invisible Narratives. The notice alleged that Garry's Mod violated the copyrights associated with "Skibidi Toilet", an animated webseries created by YouTuber Alexey Gerasimov produced in the Valve software Source Filmmaker using assets from their games Half-Life 2, Counter-Strike: Source, Garry's Mod (which Valve published but did not develop), and other pre-existing copyrighted material. The Skibidi Toilet copyrights were registered as part of Invisible Narratives' production on a film adaptation of the series directed by Michael Bay. The takedown claimed there was "absolutely no licensed Steam, Valve, [or] Garry's Mod content related to Skibidi Toilet", despite the fact that many of the assets the series uses were originally created by Valve and the Garry's Mod playerbase up to almost two decades before it existed. After Newman posted the takedown notice publicly in July 2024, Gerasimov became aware of the mistake and contacted him to resolve the issue and retract the takedown.

Later on December 18, Epic Games revealed a collaboration with Skibidi Toilet for the game Fortnite, adding the character Plungerman as a playable skin and the titular Skibidi Toilet as a back bling. Seemingly forgetting about the controversy that occurred a few months prior, many unaware fans speculated if a lawsuit could play out due to the use of Valve's assets, despite their models in Fortnite being stylized, legally distinct versions of them. After being flooded with questions asking about it, Newman became annoyed and released a statement clarifying that he had no "basis, want or need" to file a lawsuit against Epic Games or Gerasimov as he did not create any of the assets involved in the production of Skibidi Toilet in the first place, and asked the public to stop asking him about it.

In June 2022, user Isaac Macgill, the creator of the Garry's Mod add-on "Glue Library" which expanded LUA functionality with mod support, updated some of his Steam Workshop releases to display internet screamers with shock images and loud noises upon start-up. The source files in this update also included curses and threats directed at creator Garry Newman, Valve co-founder Gabe Newell, and several unidentified Steam moderators. Macgill's motive for the changes is not known, as he was quickly banned from Steam after they received numerous complaints, though some suspected it to either be a deliberate prank, a response to online harassment, or a response to a personal grievance with the platform. Similar copycat incidents occurred around the same time with add-ons based on the Trollface meme, which instead caused the game to display a different set of explicit images and play loud audio of slurs spoken in the voice of cartoon character SpongeBob SquarePants, or hampering the game's UI with images of the character Neco-Arc from the Tsukihime series.

In April 2024, Nintendo issued a takedown notice regarding its content being used in Garry's Mod, prompting Facepunch Studios to remove roughly 20 years worth of assets from the game's Steam Workshop and ask their community members to do the same in order to speed up the process. Although rumors circulated that it was actually an unrelated party issuing the takedowns due to past instances of such, the game's creator Garry Newman insisted that this was not the case, and that the takedowns were in fact from Nintendo themselves.