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.
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.
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.
Continuity mistake: When Shang Tsung has finished summoning his warriors, before the last fight with Liu, the camera zooms out showing all five warriors, you can see Shang lowering his arms to his sides. Then it shows a close-up of Shang Tsung and he has his arms in the air and lowers them again.
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.