Johnny Cage's triple head uppercut fatality was inspired by a glitch in Mortal Kombat where you could preform his fatality twice, resulting in two heads being knocked off of the opponent instead of one.
In the Genesis port of the game, Rayden has an exclusive finisher that can be activated through a cheat, called "Fergality." This turns his enemy into a smoking version of Fergus McGovern, CEO of Probe Ltd. who worked on the port of the game.
An unused graphic of the WWF logo can be found within the game's code. It's likely that it was meant for an advertisement that was scrapped.
There is an unused animation of Raiden lifting up and shocking someone. It was likely a Fatality, as Raiden would eventually use a similar Fatality in Mortal Kombat 4.
The Japanese version of the SNES release is slightly censored. All blood has been recolored green and all fatality moves (excluding the stage fatalities) cause the screen to become monochrome.
Shao Kahn had to be re-sized to be taller than the other Kombatants, as his actor, Brian Glynn, was shorter than everyone on set.
By playing 250 matches in a row, the players unlock the ability to play a round of Pong in the middle of the match. The game lasts until one player gets 7 points before throwing both players back into the match.
In the Pit II level, there are two characters fighting in the background. Fans named them Hornbuckle and Torch. In actuality, they are just resized and recolored Liu Kang sprites. Torch would later appear as Blaze in Mortal Kombat: Deadly Alliance.