In the scene where Liu Kang tells Sonya Blade to check her compass she flips open her watch face to reveal the compass. She then begins to walk off with the watch face still open, however in a split second the watch is shut again with no sign of her closing it.
After Shang Tsung tells a statuesque Reptile to watch over Princess Kitana, Reptile animates and jumps away. However, Cary-Hiroyuki Tagawa looks down at the jumping Reptile before he/it actually jumps.
When Goro defeats Art, Shang Tsung declares it a "flawless victory" which is from the video game the movie is based on. However even though losing quite badly Art did get in a few punches to Goro's torso then a flying kick to his chest which knocked him back. Clearly not a "flawless victory," which is when the loser doesn't get a single hit in.
Sonya is wearing black jeans all the time after coming to the island. When she is fighting, they are cut into shorts. Next time you see her, they are jeans again. However, earlier she embarks on the boat not knowing of the competition, so she does not have any extra clothes with her.
During the dinner scene, the masked warriors dump food off the tables and move them all aside. When the fighting begins where the tables once were, the floor is spotless with no food or table debris of any kind on it - they couldn't have cleared the tables AND cleaned the floor this quickly.
Shang Tsung's hair changes several times between shots in the first part of his fight: different strands of hair become loose with each angle change, and after he gets punched down, it's perfect again.
When Sonya is pushing her way through the crowd at the club to get to Kano, in close up shots with Bridgette Wilson her face is clean. In long shots when her double is used, it looks like she's wearing camouflage.
After the souls are released from Shang Tsung, the camera pans down to show Johnny Cage, Sonya and Kitana walking on the spiked Mortal Kombat logo where defeated Shang Tsung's body decomposed into a skeleton. However, Shang Tsung's body is missing in that shot.
During the fight scene in the dining hall (where we see Kano eating and talking to Goro), Johnny Cage pulls a weapon out of the hands of one of the guards. In the next shot of him, where he's kicking another guard in the head, the weapon is not in his hands. In the last shot of him (forcing him into Sonya's out-stretched arm to knock him out), the weapon is back in Cage's hands.
When Liu Kang has to fight the warriors after the brief fight with Shang Tsung, just before he jumps to defeat the last warrior, you can see Shang Tsung watching from the doorway. As soon as the shot goes to a wider shot and Liu Kang jumps up using the stair Shang Tsung disappears.
Sub-Zero flips down from the platform followed by Liu Kang. On the floor, Liu kicks Sub-Zero. Sub-Zero falls to the ground and after he falls he rolls once more. The kick wasn't that hard and it's clearly visible that the extra roll was forced.
During the fight scene between Scorpion and Johnny Cage in the plantation, Scorpion releases the creature from under his arm; but when he calls it back, it can be seen that the source is his palm (this happens twice in that scene).
When Sonya is chasing Kano through the crowded nightclub, not only does the henchman show no qualms about firing an automatic weapon at her while she is in a crowd of dancers, but the dancers themselves seem not to be remotely disturbed either by his shots, or by Sonya's shotgun blast.
When Sonya, Johnny and Liu Kang are leaving after witnessing the conversation between Goro and Kano, they are walking down a hallway covered in spiderwebs. Johnny Cage says 'Kitana came this way, I'm sure of it' - but he is pushing through the spiderwebs blocking the doorways. If Kitana had been through that hall not long before, the spiderwebs would already have been torn down or through.
Before the Johnny Cage vs. Goro fight, Rayden appears "magically" as Goro walks by. But the actor can be seen trying to walk in to the shot behind Goro unnoticed. He comes in just over Goro's arm in the top left corner.
The goof items below may give away important plot points.
Liu Kang erroneously announces his win against Shang Tsung as a "flawless victory", despite being hit several times including a brutal head smash to the concrete floor.
Then again, he was probably just using Shang Tsung's 'catchphrase' as a one-liner.
When Shang Tsung dies, his body decomposes and instantly becomes a skeleton on the spikes. But when the while aura of souls emerges, Tsung's human body can still be seen on the spikes - not as the skeleton he was just reduced to.