Continuity mistake: When Kung Lao and Shang Tsung are preparing to fight each other at the tournament, watch Shao Kahn. He gets up off his throne, then it cuts to wide shot and he's sitting down again. Then it shows him standing up again only to go back to sitting down a fraction of a second later. (00:03:40)
Continuity mistake: When Shang Tsung transports the scorpion we see it enter a fire coloured portal in Outworld which then changes to a blue coloured portal on Earth Realm. In all other episodes the portals in the Earth Realm are fire coloured and the ones from Outworld are blue.
Plot hole: In the Mortal Kombat storyline, Noob Saibot is the original Sub Zero after he was killed in the Mortal Kombat tournament. At this stage, Sub Zero has not been killed, therefore Noob Saibot should not yet exist.