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!"

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.

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.

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.

In Japan, Capcom sold both Red Sun and Blue Moon copies together as a dual pack.

It was previously believed that the Z Saber Battle Chip could only be accessed by trading it into the game from Mega Man Zero 3, of which each copy of the game had only one copy of the chip. However, in 2022, an easier way to obtain the chip was discovered by entering the following hidden code at the Number Trader: 72794137. This code also works in the Japanese version of the game, causing its existence to baffle players as it has never been released in any of the game's official strategy guides. It's possible that the code was intended to be used during development as an easier way to access the chip without having to trade it across games, and that it was never meant to be found by players.