The NES cover of the game shows each of the turtles wearing red masks instead of the individual colors that they wear in the cartoon and in the game. This is because the cover is a remake of the second print cover for issue #4 of the Mirage comics, where they all wore red masks.

In the DOS version of the game, there are hidden credits in the Dam level to two people named Dean and Mike, accessed only by using cheats. These people are Mike Smith and Dean Grifiths, graphics artists who worked on the DOS port.

In one of the sewer sections of Wall Street, there is a small gap in the NES version where a short jump must be performed in order to cross over and avoid the sewer water. In the DOS version, this same gap is now larger, and the ceiling is lower, making the game impossible. There is no way to cross over, none whatsoever. The only way to pass over is to use a password to skip the entire level.

The game, along with all the other Teenage Mutant Ninja Turtles merchandise at the time, was renamed Teenage Mutant Hero Turtles in most of Europe. This was due to the British government being strongly against violence in products marketed for children, including things such as ninjas. Despite this change originating from the UK it affected many other countries as well.

Despite its large grip in the US, the Nintendo Entertainment System struggled to gain footing in the British market due to botched marketing from Mattel, stiff competition from an already-established Sega, and microcomputers that had well-renowned games as cheap as £1.99. The console's fortunes in the region would turn with the release of a bundle containing the Teenage Mutant Hero Turtles video game which, despite Nintendo of America's objection to it, would go on to increase sales of the console by 2,000 percent and establish Nintendo as a player in the UK gaming market.

As of 2023, only 4 licensed IP adapted games have been released on Nintendo's retro game digital download services: Teenage Mutant Ninja Turtles for NES on Wii (which was later delisted on January 26, 2012), Transformers: Mystery of Convoy for NES on Wii, Quest for Camelot for Game Boy Color and GoldenEye 007 for N64, the latter two being on Switch.

Additionally, J.J. & Jeff, Punch-Out!! Featuring Mr. Dream, and Super Mario Bros. 2, all reskins of licensed titles, have been available in their license-less formats.