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.

In the German version, all the blood and gore was removed or censored in the intro cutscene.

At one point in development Mortal Kombat: Shaolin Monks was intended to be a single player game featuring Raiden as the only playable character.

When two players select Sub-Zero in versus mode, his player 2 outfit is recolored black, resembling Noob Saibot.

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.

Several unused enemies, as well as evidently bosses, still exist within the game's data and can be spawned in-game with a proper third-party cheating device.

A Naga-styled enemy (In Japanese mythology, the Naga is a snake-based monster with the upper torso of a vicious woman) is one notable example, as well as an anthropomorphic demonic tiger which utilized some type of area-of-effect based ice powers. Most notably of all is a towering, multi-armed Hindu-inspired being with green skin and wind-based attacks, who also has functioning "jiggle physics" coded for her breasts during certain animation frames. This unused boss noticeably towers over the player's when hacked in, filling a decent portion of the player's screen.

Although not yet explicitly stated by any developers of Shaolin Monks, it's possible that should these unused characters have made it into the final release, their designs could have emphasized the lore and world building aspects that John Tobias was publicly passionate about in the early installments of the Mortal Kombat continuity. It's equally possible that the two bosses in particular were scrapped simply due to their in-game models holding such stature that extra time and resources would need to be invested in specially designing stages which would house their positions in the linear progression of the story. Hacking either boss in as mentioned above will cause them to clip through surfaces in many of the playable environments.

A message that may sometimes appear on-screen upon achieving a Game Over is "Noob has left the build." This is a reference to the catchphrase "Elvis has left the building" (in reference to Elvis Presley), but applied to the villain Noob Saibot, who only appears briefly in this game. The message also has a play on the word "build", in reference to development builds of a video game. Tying this together, "Elvis" also has a credit in the Additional Thanks section of the game's end credits.

A message that may sometimes appear on-screen upon achieving a Game Over is "10,000,000 points if you destroy Sdrawde Lhup". This is a reference to Reptile's hidden pre-fight appearances in the first Mortal Kombat arcade title (revision 3.0) and the score bonus for defeating him. The name "Sdrawde Lhup" is made up of the backwards surnames of Adam Puhl and John Edwards, the two lead designers of Mortal Kombat: Shaolin Monks.