Contrary to popular belief, Johnny Cage wasn't cut from MK3 because his motion capture actor, Daniel Pesina, had to be fired from Midway after advertising a game called BloodStorm (developed by a different company) while dressed as his character.

In a 2020 podcast interview, Mr. Pesina stated that he wasn't fired, but rather that he left Midway because they refused to pay their actors on time. He also stated that series' co-creators Ed Boon and John Tobias assisted him with negotiating for the BloodStorm promo and what he wore in that ad was approved by Ed Boon, directly debunking the rumor.

A year later, John Tobias confirmed in a Twitter thread that the reason why Johnny Cage didn't show up in MK3 was because he was one of the least popular/played characters in the previous game, so they decided to remove him entirely, with the in-universe reason being that he died. He was later brought back for Mortal Kombat Trilogy, this time being potrayed by Chris Alexander.

There are a lot of unused sprites of Motaro left over in the game's memory, including:

• Motaro raising up his front legs.
• Motaro doing his teleport move.
• Motaro performing an arm lift as if he were going to throw the opponent over his head.
• Motaro raising his arm, along with moving mouth sprites that suggests this would be some sort of taunt.

There is also an unused win screen for him that would not show up until Mortal Kombat Trilogy. This evidence suggests that Motaro was probably going to be a playable character at one point.

Because Sheeva has four arms, a unique four-armed skeleton sprite is stored in the game's memory but is never actually used in-game. This was likely meant to be used for Kano's skeleton rip Fatality.

Shao Kahn was voiced by Steve Ritchie, who was working at Williams Electronics as a pinball and video game designer at the time.

A large number of unused items in the game's code suggests that the ninja characters were originally planned to appear in the game. These include an animality animation for Ermac, a friendship animation for Classic Sub-Zero, unused win text for Scorpion, and a debug menu with references to Sub-Zero and Smoke.

By performing Nightwolf's Friendship, he will transform into Raiden with a Mortal Kombat II arcade cabinet. He also says "I've never seen a Kano transformation," which is referring to the rumors that Shang Tsung could transform into the missing Kano in Mortal Kombat II.

Viewing the full model of the bank from the Street stage shows carvings referencing Pac-Man.

Noob Saibot's sprite in Mortal Kombat 3 is actually a blackened Kano sprite. He uses Kano's combo moves but none of his special moves. The reason for this is that there were no ninja sprites in the game.

Cyrax and Sektor were named Mustard and Ketchup respectively during development until they were finally given names.