- Flip-Flop of God: The fate of the Four Guardians during/after Zero 3. UCapcom claimed they continued to fight in some unknown place, while the MMZ Complete Works claimed they died in Omega's boss explosion. Most recently, in the MM25 Mega Man & Mega Man X Complete Works Q&A session, it was claimed that Neo Arcadia has no records of further activity from them and in-story they're considered deceased, but they could still be alive beyond its sensors.
- At the time there was a popular theory that the Mother Elf was originally a reploid (more specifically Iris from X4) based on the fact that X and Elpizo underwent a similar transformation. This theory was officially disproved in Complete Works where is stated that the Mother Elf was created from the Maverick Virus data in Zero's body.
- When Mega Man Zero 2 was released, many theorized that Omega was Sigma (or at least somebody with a close connection to Sigma), due to both names being letters in the Greek Alphabet. Come Mega Man Zero 3, we learn that he's actually Zero's original body.
- Manual Misprint: For one reason or another, the Official Complete Works lists some of the game's Mutos Reploids as "your Resistance allies".
- No Export for You: The e-reader bonus content for the original GBA Zero 3 (Averted for the DS Compilation Re-release). It can be nevertheless be enabled in non-Japanese versions via cheat codes, complete with English text.
- The Other Darrin: Both Zero and X have new voice actors that were never used in the Mega Man X series; Zero is played by Ryotaro Okiayu in X and Yuuto Kazama in Zero, while X had been played by Showtaro Morikubo up until X7 and is played by Takahiro Mizushima in Zero. Interestingly, instead of adopting the Zero series' actors, the X series continued using Okiayu for Zero and diverged into a new example of The Other Darrin for X by introducing Takahiro Sakurai to the role (from Command Mission onward).
- Postscript Season: The series was meant to end with Zero 3, as evidenced by resolving the Dark Elf storyline, giving X his eternal rest, bookending with the lab ruins, etc. And developer interviews. Of course, we got Zero 4, which turned a Postscript Season into a proper Grand Finale. Strangely, the fates of the three living Guardians after Omega's death are completely ignored until the Zero Complete Works, which says they died in Omega's explosive death throes. Z4 doesn't so much as mention them.
- Urban Legend of Zelda: It's theorized that Dr. Weil was originally going to be Dr. Wily, but the continuation of the Mega Man X series cancelled that in the event that the subplot of Wily being Zero's creator got resolved there. This is supported by their similar sounding names, Weil's knowledge on Zero's design, and with the implication that Dr. Wily was still alive in Mega Man X5 (the original finale to the X series), but was never confronted.
- What Could Have Been:
- Zero 1:
- The original X himself was going to be the Big Bad, and not just some copy. Presumably after having to deal with the maverick uprising all by himself for over a hundred years, he would have snapped and Jumped Off The Slippery Slope in the name of protecting humans. The Big Bad being a copy instead was literally a last month decision, and done because it was felt X being a canon Ron the Death Eater wouldn't sit well with the kids who played the X series games where he was the hero.
- Ciel was originally drafted as a cyborg.
- Ciel had designs for a player character role, specifically as a Cyber-Elf using mage type character.
- "Harpuia" was originally meant to be the name of the character's swords.
- Zero 2: A bat-like One-Winged Angel form was planned for Phantom to match the other three Guardians', although considering that Phantom had already been killed off, it may have simply been drawn on a whim. See here.◊
- How the Dark Elf comes to be: during early conceptions (as mentioned in Official Complete Works), the Maverick Virus' influence overwhelmed the Mother Elf, causing her to turn "dark", as opposed to Weil altering her programming.
- Zero 3:
- Young, middle-aged, and elderly (i.e. the final version) designs were drafted for Weil. The young version had a Mini-Mecha while the middle-aged version had a hairstyle resembling Dr. Wily's.
- Omega's second form would have been much more active (for example, actually using its BFS) if not for GBA's graphics limitations.
- The series was originally meant to end with the third game, with Dark Elf now free, X finally retiring into Cyberspace, and Omega being destroyed for good. Thankfully, they changed the Post-Script Season that is Zero 4 into an epic Grand Finale (though with some Fridge Logics here and there).
- Volteel Biblio's design is adapted from an older design for a electric eel boss.
- Similar to the above trivia about Copy X, Omega was intended to be the original Zero Brainwashed and Crazy, and The Reveal would be that, instead of being in an imitation body, you yourself were an imitation of him, a sort of "Copy Zero". This was changed after the Executive Meddling that gave birth to Mega Man X6, since Zero's sudden revival would have turned this into a plot hole.
- Zero 1:
Trivia / Mega Man Zero