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: At the beginning of the film directly in front of Sonya a brick pillar falls down. It cracks and you can see bits of uncolored foam.
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 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: When Rayden and Kahn fight at the start of the film, at one point Rayden does a flying body-spear into Kahn, which sends him flying backwards. When he lands on the ground, the floor beneath him "warbles," revealing he landed on a pad. It also continues to move a bit for the rest of the shot as he moves.
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 easy to miss the first time, but if you know to look for them, they're pretty obvious. You can see similar lines in the sky in several other shots throughout the scene, but it's most noticeable here.
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 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 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.
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).
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.