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.
Continuity mistake: In the scene where Sonya fights Malena, the amount of mud that Sonya gets on her increases and decreases throughout the fight.
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.
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.
Continuity mistake: When Sonya grabs Ermac with her legs in the final battle, pay close attention. In one shot, you can see for a brief instant that Ermac's mask has completely fallen down and his entire face is exposed, but two quick cuts later, his mask is suddenly back on. (It goes by quick so you have to pay attention, but it's very noticeable once you see it the first time).
Continuity mistake: When Rayden says the line "What closes can also open again" in the beginning of the film, watch the background. For this one single shot, the top of the pillar behind him on the left is missing a square-shaped chunk. But in the shots of Rayden before and after, the pillar is totally intact.
Continuity mistake: During the Cyrax vs Jax fight, at one point Jax gets knocked to the floor and says "Yo, I take it this ain't something we can talk about?" If you watch, when the camera cuts from a wideshot of him landing to the closeup of him on the floor saying his line, he's suddenly in a completely different spot on the floor and the debris behind him is totally different.
Continuity mistake: During the Liu Kang vs Baraka fight, at one point, two more Barakas swing down on chains. Liu kicks them off the chains, and they simply disappear for the rest of the scene. They didn't fall into the firepits, as you can hear them hit the ground, nor would the fall have killed them, as they aren't high off the ground. They simply... disappear.