In the U.S. and European versions of the game D. Dark's punch grab move was censored and replaced with a generic throw, his original grab move was to slit his opponent's throat. The code for the animation can still be found in the game.
The move is also censored in the prefectures of Odawara and Niigata due to stricter regulations in those prefectures.

In the Japanese version of Street Fighter EX Plus Alpha, D. Dark's kick grab move used an explosive on the opponent's throat. This was censored and replaced with a generic throw in the International version.

As shown in early footage, some characters had different names, color palettes and/or hairstyles. For example: The character Allen Snider had a different color palette (having blond hair and wearing a red gi with black, rather than the orange hair and purple gi of the final version) and he was originally called "Cashew Snider". Also, it looks like at one point they were going to use remixed music instead of new compositions, judging by the character select and Ryu themes.

Two of EX's unlockable characters, Blair Dame and Allen Snider, appear in a non-Capcom fighting game named Fighting Layer, created by EX's developer Arika and published by Namco. Interestingly, neither of these characters appeared in the subsequent Street Fighter EX titles, unlike the rest of EX's characters.

Skullomania was originally referred to as "Rubberman" in concept art, most likely because the character's bodysuit resembled rubber.

Allen Snider was once modeled after singer Elvis Presley, and was even referred to as Elvis (エルビス) in concept art, where he had blond hair and was shirtless.

The team originally thought about giving Darun Mister the abilty to grow his moustache more and more with each victory, but the idea was never used.

The cycloid were created with the intention to give a "strange vibe" to the players. Cycloid – β, in particular, was designed in order to see if the development team could introduce elements such as mirror surface processing, refraction of light through transparent objects, and representation of flames, all of which were very popular elements in programming around the time of the game's release.

According to the "ALL ABOUT Capcom Fighting Games 1987-2000" book, Kairi was originally supposed to be the main character of the EX games, but the idea was scrapped and Ryu was choosen over him.