Revealing mistake: In the swimming pool scene, when David is sitting at the bottom of the pool, you can clearly see a scab on one of his knees. (00:43:00)
Audio problem: After the aeroplane crashed, a dinosaur stepped over it and the windows shattered making the typical sound of made-of-glass things when broken. They are made of plexiglass (a sort of fibrous plastic).
Plot hole: The "video history" of the crashed USAF ship makes it very clear that the planet is uninhabited when they "landed". I can understand how a race of apes develops - they had a bunch of them on board. I can understand how a race of humans develops - they are descendants of the original crew. What I don't understand is...where the heck did all the horses come from?
Continuity mistake: In the beginning scenes, where Milo Thatch is practising his proposal, he slides over (face forward, chest against the board) a chalk drawing of a map detailing the location of Atlantis. When he realises he wiped off the drawing, and sees it on his clothes, he stands in front of the blank part of the chalkboard, "filling in" the space with the map that rubbed off on his shirt - the only problem is, that the image should have rubbed off backwards as he was facing the board when it transferred to his clothes. He could not simply stand in the place of the missing map face forward and have it read properly.
Continuity mistake: During the fight with Gabe and Yulaw, Yulaw does a powerful move of lunging forward and smashing Gabe with both his fists, sending him flying into a green metal box that crumbles from the impact. Gabe then falls to the floor, close to the box. The shot changes to Yulaw thinking he has victory, then back to Gabe. Gabe is now noticeably further from the green box, and his arms and legs are in different positions. (01:08:40)
Continuity mistake: When Juni handcuffs the metal box to his wrist, it switches back forth from his right wrist to his left over and over again. (00:35:05)
Continuity mistake: During the scene in the mall when the girl is in the dressing room, she keeps putting on more layers of clothing. But as they are shooting different shots she will have a hot pink shirt on, then it is back on the hanger, and then back on again. It switches back and forth many times. (01:00:50)
Factual error: In the begining at the bridge ceremony, the band plays Manhattan Beach by John Philip Sousa. However, Manhattan Beach was composed in 1893. (00:00:50)
Continuity mistake: When the panel of doctors are being queried by Aames, for the second time of the loop of this interview, the black box containing the mask can clearly be seen in the bottom right hand corner on the desk when the camera swings to the main doctor. When the camera pans back again, it is gone, and it is only after this that the assistant brings in the box.
Continuity mistake: Nick's necklace is a string looped through a ring, but sometimes the string makes only one pass through the ring and sometimes two.
Continuity mistake: The grandfather, father, and son all have VERY blue eyes, but in the flashback scenes, the actor playing the grandfather as a young man has very dark eyes.
Continuity mistake: When Remy falls through the barricade she is wearing a G-string, but when she strips down to mix up the scent she is wearing different underwear.
Continuity mistake: Right after Aki saves Gray and turns around to pick up the canister containing the plant off a table there is no table or ledge. If you watch the movie with the commentary one of the members involved with the movie says that it is floating on nothing. (00:16:50)
Revealing mistake: Have a look at the shot of the rear part of the train exploding as the locomotive pulls away from it. If there was ever a more obvious model shot, with cheesy, jerky bouncing toy trains and Action Man (TM) dolls, then I haven't seen it.