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'.
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.
Revealing mistake: When Liu transforms into a dragon during the final battle, the wideshot where he actually transforms while being held by Kahn is completely laughable. The digital dragon clips through portions of the live-action background (particularly around Khan's arm that was hanging onto Liu) and the lighting on the dragon doesn't match with the lightning flashes in the background.
Revealing mistake: When Smoke is running up to Kitana at the start of the Liu VS Smoke fight, Liu runs up behind him, jumps and pushes his foot against a pillar to sort of rebound, and grabs Smoke. There's a quick insert shot of Liu's foot pushing against the pillar, and you can see the "stone" pillar briefly bend like rubber beneath his foot, revealing it's fake.
Deliberate mistake: When Jade is killed, Kahn is holding her up by her neck about a foot above the ground as the monster appears behind her. Right before the monster bites down and eats her, Kahn lets go over her neck... and she just sort-of floats in place. She should have fallen back down given she was being held above ground. (In all likelihood, the actress was standing on a box or something to make it look like Kahn was holding her up.) This happens a bit quickly, so it can be hard to catch.
Continuity mistake: When Sonya grabs Ermac with her legs in the final battle, pay close attention. In one shot, you can see for a brief instant that Ermac's mask has completely fallen down and his entire face is exposed, but two quick cuts later, his mask is suddenly back on. (It goes by quick so you have to pay attention, but it's very noticeable once you see it the first time).
Revealing mistake: During the Jax vs Cyrax fight, pay attention right after Jax says "Yeah, now what?!" A few shots later, Sonya is hit in the face with a weapon by one of the extermination squad members. But you can see plain as day that the weapon completely misses her. It actually goes over her head, but she still reacts as though she's been hit in the face.
Revealing mistake: During the Liu VS Baraka fight, pay attention when Liu and the Barakas are swinging around on the chains. Several times, you can see safety-wires attached to the chains and actors. It can be hard to catch, but there are at least three or four shots where they are visible.
Revealing mistake: When Sheeva is crushed by the cage, pay attention to the first shot as we see the cage falling towards her. You can see the cage actually come to a stop right before it cuts to the low-angle shot looking up at her screaming. (Since it would be rigged to stop above the actress so it wouldn't actually crush her. They unfortunately just cut the shot too late).
Deliberate mistake: During the opening fight between Rayden and Kahn, at one point Kahn is kicked and lands on the ground in front of his generals. A few seconds later, he is hit and lands on the ground again... in the exact same spot, landing in the exact same position. (Watch for the somersault he does.) It's clear these are two different takes of the same stunt. It wouldn't necessarily be a mistake, except when he gets hit the second time, he flies backwards a bit, so it makes no sense for him to land in the exact same spot as before. Sloppy editing.
Continuity mistake: When Rayden says the line "What closes can also open again" in the beginning of the film, watch the background. For this one single shot, the top of the pillar behind him on the left is missing a square-shaped chunk. But in the shots of Rayden before and after, the pillar is totally intact.
Revealing mistake: When the Emperor's generals are introduced at the start of the film, pay attention to Sheeva's lower arms. If you look closely, her lower arms are added digitally and don't quite blend with the actress, nor do they 100% match her motion. (Especially her lower-right arm, which is on the left hand side of the screen. You can see it "clipping" with the background plate. At one point, it even briefly looks like it's floating behind her for a moment instead of being attached to her).
Revealing mistake: Jax and Sonya jumping away from the explosion when Cyrax self-destructs is just comical. The lighting on their bodies doesn't match the lighting in the background, revealing they were just filmed on a green-screen, and the background makes no sense whatsoever. The background is a blurry still image that doesn't have the same color-temperature as the exterior of the base seen earlier, with an obvious stock-explosion effect added over top of it that doesn't blend properly into the scene.
Revealing mistake: During the Jax vs Cyrax fight, at one point Jax gets knocked down to his knee, and then Cyrax kicks him, causing him to fly upwards and backwards and roll over the top of the metal gurney. Except you can see plain as day that Cyrax's kick completely misses Jax. He kicks his leg about two feet in front of Jax's head.
Revealing mistake: When Sonya is facing the "extermination squad" while Jax fights Cyrax, watch closely. At one point, a ninja clad all in black does a jump-kick, which knocks Sonya back. Except if you look closely, he doesn't actually kick her. (It's really obvious when the camera cuts to a side-view and you can see he doesn't have his leg extended.) But they still add in a kicking sound and have Sonya react as though she's been kicked.
Continuity mistake: During the Cyrax vs Jax fight, at one point Jax gets knocked to the floor and says "Yo, I take it this ain't something we can talk about?" If you watch, when the camera cuts from a wideshot of him landing to the closeup of him on the floor saying his line, he's suddenly in a completely different spot on the floor and the debris behind him is totally different.