Revealing mistake: Cyras appears, who launches two spherical bombs that attach to the walls and explode. Watch very closely. There is a low angle shot pointed towards a doorway right after they explode, and you can see the set wall visible shake for a brief instant from the pyrotechnics. It can be hard to catch, but once you see it, it's very obvious.
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.
Revealing mistake: During the Scorpion VS Sub-Zero fight, at one point, Scorpion kicks Sub-Zero and he almost falls into a lava pit, falling and wedging himself next to a stone pillar. (It's the bit where Liu has to jump across to save him.) When he hits the stone pillar, it wobbles like it's made of styrofoam, revealing it's not really stone.
Revealing mistake: In the beginning of the film, watch closely when Sindel says the infamous line "Too bad YOU... will die!" When Sindel says the words "will die," two of her teeth suddenly turn gray and become blurred. (One tooth on top and one on the bottom.) The best I can figure is that it was some sort-of slip up with the special effects rendering, since the background has a CGI sky replacement effect. It can be hard to notice at first, but if you know where to look, it's pretty obvious.
Plot hole: Kahn's death makes no sense. In the film, Rayden explains that the dragon tattoos flee one's body upon the person dying. And yet, Kahn is still alive and not even close to death when his tattoo flees. (Which is what kills him, since it rips him open when it flees.) It's like they couldn't figure out how to kill him in the script, so he's just spontaneously is killed by his tattoo, even though it violates the rules the film set up.