- Crossdressing Voices: Megumi Ogata provides the voice of X shouting "Hadouken!".
- Dummied Out: There's a scrapped sprite of Vile where he is using a buster identical to the X-Buster. Mind you he still has his shoulder cannon, meaning it was probably removed for being overkill.
- Fan Translation: A ROM hack that retranslate the game's Japanese script based on NectarHime’s retranslation script with elements of Hondoori Game Center’s and Her-Saki’s translations is available for the SNES version of the game.
- No Export for You: Europe almost didn't get the game on the Wii U Virtual Console service, with the game being released on the Japanese and North American services within a week apart. Thankfully, this was finally rectified on September 19, 2013 and released over there.
- What Could Have Been:
- Zero's design was originally X's, but the team feared that players wouldn't react well to such a radically different design. Thus, X was given a look that resembles the classic Mega Man more, while Zero was made a separate character.
- In early screenshots, the "X" symbol on X's life bar was a "P," presumably meaning "Power." X is also seen running through a white city, possibly an early version of the Highway intro stage.
- There's old Gamepro footage depicting the silhouette of an unused manticore Maverick boss.
- There's concept art for a female Navigator, years before Alia's introduction in X5, but the team scrapped her since they couldn't figure out how organically work her in. An unnamed Navigator was worked into the X1 remake, Maverick Hunter X.
Defeating some Mavericks will affect other stages:
- Chill Penguin - freezes Flame Mammoth's stage
- Launch Octopus - floods Sting Chameleon's stage
- Storm Eagle - causes rolling blackouts in Spark Mandrill's stage (The Death Rogumer, Storm Eagle's airship—it's also the same airship Vile arrives and escapes in during the intro stage—crashes into it)
The Boomerang Cutter weapon is somewhat useful against two Maverick bosses other than Sting Chameleon:
- Launch Octopus - hit him a few times and his tentacles get cut off. In the SNES original, all his tentacles get cut off making him unable to use his life drain and homing torpedoes attacks. In the Maverick Hunter X remake, it was nerfed a bit by leaving him with a pair of tentacles, so he is still able to life drain but can only launch a pair of homing torpedoes at a time.
- Flame Mammoth - hit him a few times and his trunk gets cut off. Not really as useful since it only prevents him from throwing oil globs, but it does make him look funny.