Continuity mistake: Shao Kahn removes his cape in the final battle. When Motaro breaks Jax's bionic arm, holds it up and Shao Kahn shouts "Yes!", Shao Kahn is wearing his cape again.
Revealing mistake: At the end of the Sub-Zero vs Scorpion fight, Liu Kang jumps over to help Sub-Zero and Scorpion teleports away. A few moments later you see a shot where you see all the actors, (Liu Kang, Sub-Zero and Kitana), if you look closely you can see Scorpion waiting in the background just waiting to pop up and snatch Kitana.
Continuity mistake: During the Liu vs Baraka fight, Liu kicks Baraka into a firepit. However, the footage used to show Baraka falling into the flame is the same as the footage used earlier to show the ninja Rain falling into the fire pit.
Continuity mistake: When Scorpion and Sub-Zero are about to fight we clearly see Scorpion with white contacts over his eyes, but during the fighting you can tell the actor/stuntman playing Scorpion does not have any white contacts in.
Audio problem: At the start of the movie when Shao Kahn and Raiden are fighting, Shao Kahn smashes Raiden into a pile of bricks. Then Shao Kahn says "You will never win". Watch when he says it because his mouth doesn't move.
Revealing mistake: At the beginning of the film directly in front of Sonya a brick pillar falls down. It cracks and you can see bits of uncolored foam.
Continuity mistake: In the scene where Sonya fights Malena, the amount of mud that Sonya gets on her increases and decreases throughout the fight.
Revealing mistake: When the robotic character Smoke fires a missile that destroys a large structure in the underground cavern during his fight with Lui, if you look closely, when the explosion occurs, you can actually see additional "phantom" debris exploding upwards (from two independent bursts) from underneath the fog in front of the actual explosion, obviously to make it seem more dramatic. These secondary bursts also noticably occur several seconds after the initial explosion.
Continuity mistake: At the beginning, Raiden's hair is loose, but when he somersaults to fight Shao Kahn, it is tied up. It is loose again after the fight.
Revealing mistake: When Sonya grabs Cyrax's back and throws him into the wall (towards the end of their fight), you can see his back, supposedly made of metal (he is a robot), bend like rubber.
Deliberate mistake: When Sonya finishes Mileena, Mileena's shoulders are muddy and she is face down, but when we have a close up of the dragon tattoo the right shoulder is cleaned off and what mud is left is dry. (00:42:25)
Continuity mistake: Somehow right after the mud fight Sonya is completely clean and dry minutes later. Yes she said she wanted to find a river and clean up, but her white shirt wouldn't have cleaned like that in a river.
Revealing mistake: When Rayden and Kahn fight at the start of the film, at one point Rayden does a flying body-spear into Kahn, which sends him flying backwards. When he lands on the ground, the floor beneath him "warbles," revealing he landed on a pad. It also continues to move a bit for the rest of the shot as he moves.
Revealing mistake: During the opening scene, a few shots after we see the Outworld ninjas falling through the portal and leaping about, there's a shot of several monks fleeing that tilts up towards the (digitally replaced) sky. As it does this, you can see several hard lines about in the sky from where pieces of the digital animated skies were "stitched together." It's easy to miss the first time, but if you know to look for them, they're pretty obvious. You can see similar lines in the sky in several other shots throughout the scene, but it's most noticeable here.
Revealing mistake: During the opening scene, when the ninjas begin to arrive through the portal, in several shots as they leap about, you can tell the stuntmen were filmed in front of a greenscreen and crudely "cut out" and placed over the footage. They're very strange-looking and have a weird jagged border around them. Some of them are also missing pieces of themselves or look like they were improperly "cut out."
Revealing mistake: When Smoke is frozen and then is kicked into the pit where he explodes, watch closely. In the second shot of the explosion, once the plume of fire clears, you can see a strange-looking flame at the bottom of the screen moving subtly from right-to-left in a very unnatural way. Obviously a part of the explosive charge that created the effect. (Likely some sort-of mortar or something similar that propelled the fire upwards and is still burning).