Hakushon Daimao was removed from the North American release of the game due to licensing issues. He is the only character who was cut from the game.

Both Phoenix Wright and Franziska von Karma were planned to be fighters in the game, with Franziska being the more wanted as her whip would have been easy to implement. However, Phoenix had only one move planned, "Objection!", which the developers had trouble balancing since the attack became larger when translating the 4 letter "異議あり" (Igiari) to the 10 letter "Objection!".

Capcom's rights to Tatsunoko's characters expired, resulting in Capcom no longer being able to sell or produce copies of Tatsunoko vs. Capcom physically or digitally.

Jun the Swan's Arcade ending is a reference to Chun-Li's ending in Super Street Fighter II. In both games the player is given the choice to either have the character continue fighting crime, or lead a normal life.

When choosing candidates for the Tatsunoko and Capcom character rosters, the development team were given free reign to nominate any character they wished. However, the team faced limitations on its Tatsunoko candidates; Niitsuma explained, "[We] had to consider licensing issues. Once we had that list we had to figure out how to make a balanced fighting game. On top of that we wanted a good balance between male and female characters."

Among the Tatsunoko candidates, the team considered the eponymous characters of Muteking, The Dashing Warrior and Nurse Witch Komugi, but they were eventually scrapped. The team also disallowed characters from Genesis Climber MOSPEADA or Samurai Pizza Cats, despite the high number of fan requests for the latter.

As for Capcom candidates, the development team hoped to include Arthur from Ghosts 'n Goblins, Ingrid from Capcom Fighting Evolution, Charlie Nash, Ibuki and M. Bison from Street Fighter, a Tyrant (unclear which one specifically) and Leon from Resident Evil, Date Masamune from Sengoku BASARA, Hsien-Ko from Darkstalkers, Zero Gouki from Cyberbots, Tiara from Gaia Master, Rouge from Power Stone, June from Star Gladiator, and Nero from Devil May Cry.

In the "Training Stage", the theme has lyrics in the Japanese version, but not in other versions.