If the game detects that it is being played on a catridge copier, you won't be able to run, jump, or shoot in the game, technically making the game unplayable.

There were plans to release a Game Boy Color version of Jet Force Gemini in 2000, but the game was cancelled before it was even be announced, likely because previous Game Boy Color versions released alongside their Nintendo 64 counterparts (Perfect Dark and Conker's Pocket Tales) were received with low interest. In 2006, a prototype of the game was found and was said to be "nearly complete."

In an October 2012 interview, former Rare designer and producer Martin Wakeley said, "Jet Force Gemini on the Gameboy was the only occasion I can remember Rare outsourcing anything. It was being done by Bits Studios and was nearly done last time I saw it, I'm not sure what happened to it."

Originally, Juno and Vela were going to be kids, but after a focus group played the game, they "had trouble relating to the Kewpie doll appearances of the heroes." Rare responded with scrapping their old look in favor for the "superhero" appearances shown in the final game.

Vela's old model wasn't completely removed, however. Her character model can still be seen in the game's cinematic ending, kicking a red ball around.

Rare's old website mascot, Mr. Pants, makes appearances in the game. His most notable cameo is a cheat called "Pants as Ants" that can be unlocked by collecting 300 Ant heads, which if toggled replaces the standard blue-ants with Mr. Pants. Mr. Pants is also drawn on one of the walls in a hallway in the Tawfret Castle level.

Beating the high scores on the two "Jeff & Barry Racing" games (30 seconds for the first, 40 on the other) will unlock a track for multiplayer mode. The track is that of Greenwood Village from Diddy Kong Racing, which Paul Mountain, the lead programmer, had previously worked on before this game.

According to the Lead Programmer, Paul Mountain, the entire game took elements from different games. It had Super Mario 64's open world and free-roaming nature for scale, Quake-style "attack and cover" mechanics, and Super Metriod's collecting and upgrading of weapons.