In Japan, Capcom sold both Red Sun and Blue Moon copies together as a dual pack.
All of the Soul Unisons except for Aqua and Proto Soul have different color sprites for a karma system. However, Soul Unison is disabled when MegaMan is dark, and the light sprites also go unused.
All three versions of the game (Japan, North America and Europe) feature different logos, and the title screens of each were changed to reflect this.
There is a small sidequest that can be done in the Undernet that involves main characters Django and Master Otenko from the Game Boy Advance game Boktai. The voice clip for Otenko's signature yell "Taiyoh!" was removed from the international versions of the game.
Red Sun and Blue Moon are infamous for their many, many spelling and grammatical mistakes. Throughout the game, characters will say "a viruses" or "viruses is" instead of "a virus" or "viruses are". "To" and "too" are of mixed up, and there are various single letter mistakes like "It looks live we've been kidnapped" and "Loosing the DarkChip and ShadeMan." Certain lines are also just translated poorly, such as "MegaMan, is the jack out now!"