- Crossdressing Voices: Megumi Ogata provides the voice of X shouting "Hadouken!".
- Fan Nickname: The game is often known as X1 to differentiate itself from the series as a whole.
- 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.
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.