When the player defeats Inferno Scorpion in the NetherRealm, there's a cutscene of Kung Lao putting Scorpion into the lava pit. As Scorpion is being dragged down by undead skeletons, he sinks down with a thumbs up. This is a reference to the end of the film Terminator 2: Judgment Day, where the Terminator dies in the vat of molten steel, while giving John & Sarah Connor a thumbs up.
When two players select Sub-Zero in versus mode, his player 2 outfit is recolored black, resembling Noob Saibot.
At one point in development Mortal Kombat: Shaolin Monks was intended to be a single player game featuring Raiden as the only playable character.
A hidden survival mode can be found in the foundry stage. It was apparently never finished, and was removed from the main menu. However, it can still be accessed in-game through a long and complicated procedure.