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.
(at around 3 mins) When Sonya is pushing her way through the crowd at the club to get to Kano, in close up shots with Bridgette Wilson-Sampras her face is clean. In long shots when her double is used, it looks like she's wearing camouflage.
(at around 27 mins) 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.
(at around 1h 21 mins) 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.
(at around 49 mins) During the fight in Scorpion's tomb, a hole in the rear of Johnny's pants disappears.
Jax's name is misspelled as "Jaxx" in the end credits.
The Chinese put the family name first, which makes it odd that when Chan calls to his brother in the beginning he shouts "Liu", when this is their common name. He should have shouted "Kang" instead, when referring to his brother. Kang is a Chinese name meaning "healthy". This a dream sequence that Shang Tsung is using against Liu Kang. He is obviously missing with Liu Kangs head, and this is not reality, so him calling out incorrectly is result of Shang Tsung messing with Liu Kang, and can't be judged as reality.
(at around 36 mins) 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.
(at around 19 mins) When Johnny, Liu, and Sonya are talking to Rayden on the deck of the boat, the night sky and stars in the background are clearly black drapes with lights. The folds in the cloth can be clearly seen.
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.
(at around 1h 14 mins) During Liu Kang's fight with Reptile, when Liu Kang throws Reptile against the wall, you can see the wall bend under the weight, as if made of wood, not stone.
(at around 1h 13 mins) During Liu Kang's fight with Reptile, Liu is thrown against a stone stairwell which clearly bends under his weight, like a padded mattress.
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).
(at around 1h 6 mins) When Goro crushes Johnny Cage's sunglasses, there is a clear sound of glass breaking but when he throws them to the ground, the lenses are intact.
(at around 24 mins) 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.
(at around 54 mins) When Sub-Zero and Liu Kang are fighting on the higher platform, they switch places. Sub-Zero walks to the right and Liu does a spin kick; the kick is dodged but there is still the sound of an impact.
(at around 46 mins) During the fight scene in the woods between Johnny Cage and Scorpion, a white car is seen driving in the background on the left of the set.
(at around 4 mins) 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.
Scorpion opens the portal into the Neatherrealm for Johnny Cage to enter. The portal then closes.
After the fight between Johnny Cage and Scorpion, it's never explained how Johnny Cage escaped from the Neatherrealm. It's likely Rayden came and got Johnny Cage. It's clear in the film that Rayden can open portals, just because he can't interfere in the tournament, doesn't mean he can't go get his fighters. This scene was also added later as confirmed by trivia, so there was never a explanation because it wasn't in the original film, and was added later.
After the fight between Johnny Cage and Scorpion, it's never explained how Johnny Cage escaped from the Neatherrealm. It's likely Rayden came and got Johnny Cage. It's clear in the film that Rayden can open portals, just because he can't interfere in the tournament, doesn't mean he can't go get his fighters. This scene was also added later as confirmed by trivia, so there was never a explanation because it wasn't in the original film, and was added later.
Johnny Cage disappears during Liu Kang's fight with Reptile. It doesn't seem likely he would just leave Liu to fend for himself in battle. Johnny Cage is not allowed to interfere in the tournament, and if he tries to fight reptile with Liu Kang, earth would lose the tournament instantly because Johnny Cage would have broken the rules, Johnny Cage wasn't just standing around, he was following the rules of the tournament, and he would have known this, because Rayden would have told him.
(at around 58 mins) 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.