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.

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.

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.

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.