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.
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.
Visible crew/equipment: When the purple ninja 'Rain' is smacked into the fire pit by Shao Khan, look closely as the body falls into the pit. A stage helper's hand comes up to catch the falling 'body'.
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 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).
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)
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 hard to miss the first time, but if you know to look for them, they're pretty obvious.