The Japanese and international releases have very different title screens. This marks the beginning of a trend that would last for every single game in the series. Also, the European release does not feature the Capcom USA copyright, as that version was published by Ubisoft.

In the Japanese version, if the player reaches an area before the game requires it, the game will display a message translating to "No message." This was blanked out in the US version.

When you enter Yai's house, the rug next to her sofa makes a strong resemblance to Pikachu from the Pokemon series.

Canonically, MegaMan.EXE has green eyes. Even though the game's box art shows MegaMan.EXE with green eyes, his mugshot in-game has blue eyes. This was corrected in all sequels.

A poster outside of the DenTown movie theater advertises a movie called "Upgrade Impossible 3", starring Rom Cruze. This is a parody of the movie "Mission Impossible 3", starring Tom Cruise.