Continuity mistake: When Johnny Cage is fighting Scorpion, and he does his human spear, Johnny runs until he stops at the tree. The spear then catches up, and becomes wrapped around the tree in front of Johnny. When the camera changes view, the spear is just leaning on the tree. The camera changes view again and the spear is wrapped around the tree again. When Scorpion pulls the spear back, it goes straight back, and doesn't unwind around the tree.
Visible crew/equipment: When Kitana, Lui, and Johnny are heading towards the Black tower in Outworld, or when Kitana is explaining that Outworld used to be a beautiful place (same time) there is an overhead shot and you can see the shadow of a man on a wall holding a boom microphone.
Revealing mistake: When Sonya grabs Kano with her legs, the tape is obviously sped up.
Other mistake: When Johnny Cage is fighting Scorpion in the forest, after Scorpion unleashes his snake-like spear from his hand but before the camera switches to Johnny, you can see the spear move down and it appears to be coming out of his forearm. Also the hole in Scorpion's hand from the spear is now gone.
Continuity mistake: In the final fight (Liu Kang vs Shang Tsung), after Liu Kang has defeated the five people Shang Tsung made appear, Liu goes to the middle of the floor (and MK logo) and says "Is that all you've got, sorcerer?" Immediately after this line, the camera angle (and shot) changes, and if you pay attention to the MK logo on the floor, notice that Liu Kang turns 90 degrees between the shots without taking a single step. (01:20:35)
Continuity mistake: When Liu Kang fights Sub-zero, Liu Kang stands in a fighting position with his left hand in front of him while Sub-zero generates a lot of ice. Just before the ice hits Liu Kang, the shot changes and Liu Kang stands opposite with his right hand in front of him. (00:53:05)
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.
Continuity mistake: When Kano is talking to Goro, he is drinking from a large goblet, and it is the only one on the table. Goro knocks the drink onto Kano's lap, and the camera cuts to Goro saying, "How lucky for them, back home." The camera cuts back to Kano and the goblet is sitting back on the table. The camera cuts to Shang Tsung entering the room and back to Kano with the goblet correctly missing.
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).
Audio problem: Right before the film ends, the giant spectral Shao Khan says the line "You weak, pathetic fools! I've come for your souls!" His mouth more-or-less matches "You weak, pathetic fools!", but it doesn't match "I've come for your souls!" in the slightest. (It looks as if he's saying something else entirely, and they dubbed in a new line in ADR).
Continuity mistake: During the ending, watch Liu and Kitana closely as Raiden says the line "I've been looking for you! What took you so long?" Kitana has her arm around Liu's, but lets go and stands a few feet away from him. The camera then cuts to a medium-shot of Liu and Raiden talking. (Kitana is not visible in this shot, as she is standing several feet away.) Then, the camera cuts again to a wider shot, and suddenly Kitana is standing literally right next to Liu and has her arm around his once again.
Other mistake: As Reptile falls backwards over the table, you can see the brand name of the sneaker he is wearing on his right foot.