Revealing mistake: When Sonya grabs Kano with her legs, the tape is obviously sped up.
Revealing mistake: When the three heroes are confronted by Subzero and Scorpion on the junk, Scorpion extends his living grappler hook from his hand. As he does so, the hook does not quite move in synch with the hand, indicating its origin as inserted computer image.
Revealing mistake: When Scorpion explodes, if you pay attention, the explosion doesn't really make "sense." The first "burst" looks fine, but then, midway through the shot, some of the debris in the air suddenly vanishes or fades out a few frames before the second "burst" occurs. Additionally, the way the second "burst" happens gives it away as an added effect, as it doesn't really overlap the background properly. (It looks like an explosion that was filmed on a blue-screen and then just added over top of the footage, as it doesn't interact with the environment properly).
Revealing mistake: Watch closely when Scorpion breathes fire at the end of his fight with Johnny Cage. In the wide profile shot where we see the "stream" of fire shooting out and hitting Johnny's shield, if you look very closely, you can kind of make out some sort-of "structure" within the flame. It looks kind of like a pole. It looks like to accomplish the effect, they lit a "flame bar" or pole on fire so the flames would travel upwards, then comped it into the scene and rotated it using special effects to make the flames look like they were shooting sideways. Unfortunately, the pole/flame bar is still just barely visible in the film. (It's much easier to see on the Blu-Ray version, but can be made out on the DVD).