Drahmin's design gave the developers problems. In early development, the club on his right hand switched to his left hand when he faces a different direction. They had to create special codes so that it would stay on his right hand.

The character Bo' Rai Cho's name sounds like the Spanish word Borracho which translates to "drunk", aptly describing his nature and Drunken Fist fighting style.

Mavado's design originally resembled a matador, as part of an overall Spanish theme -- his name was "Malvado", meaning "evil man" in Spanish and Portuguese. This was changed because the developers felt that his appearance didn't fit in with the Mortal Kombat universe, and they redesigned him to give him a darker persona.

Cyrax is able to perform a combo named "Full Gore". Given that fact that Cyrax is a cyborg, this is likely a reference to the cyborg Fulgore from Killer Instinct, a game inspired by the popularity of Mortal Kombat II.

In Konquest Mode, remaining idle on dialogue screens at certain points will cause a monk towards the bottom of the screen to break the fourth wall; turning around to look at the player and shrugging before resuming his original position.

There are three unused Announcer voice clips found in the game's code, one of which announces the name of the non-playable sub-boss Moloch. This was found grouped with character selection screen data, suggesting that he was once planned to be included as an unlockable playable character. There are also two humorous voice clips shouting "Fat!" and "Fantastico!" that may have been recorded as inside jokes, but their intended purpose remains unknown.