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.
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.