The Japanese Version contains 2 lines during one of Megaman's winning poses not present in the Western Versions, where Dr. Light will either simply congratulate him or offer him cake. These lines were later restored for the Playstation Version of the Game.

In the Japanese version, Morrigan has a victory pose that shows her in a revealing dominatrix outfit along with Lilith tied up with a rope, which was censored in the International version. However, her victory pose does appear in the International version of Marvel vs. Capcom 2: New Age of Heroes.

In the games files are graphics for an unused assist character. This was Tomichin, a cartoon character invented by one of the game's developers.