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.
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.
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.
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 Rayden and Khan face off at the beginning, when Rayden says "As long as I have the power, Khan...", look at the background. The tree and pillar behind them look very crude, with fuzziness and haze around them from where they were rotoscopped so the background could be added behind them.