Other mistake: At the end of the film when they arrive in NYC looking for the library, we know that they survived because they are inside with a roaring fire burning. But where is the smoke up above, as Jack Hall approaches? There must be a chimney, or else they would have all died of asphyxiation.
Continuity mistake: When surrounded by police and a garbage truck, Frank drives his car from the overpass onto the passing transport trailer below, then lands behind a hatchback and in front of two cars - a white compact with a sunroof and a grey hatchback. In one specific shot from atop the trailer, as Frank rolls his window down (before he requests the gun) the only vehicle behind Frank's car is the white compact, which is at the trailer's rear. Note things such as the trailer's safety bars, and the view through the compact's windshield for starters. That grey hatchback is back when the ramp is lowered, for the ensuing crashes. (00:08:20)
Revealing mistake: When the UFO makes the huge flash that knocks everyone in the cemetery down, one of the police officers kicks a tombstone as he falls and it wobbles back and forth. (00:13:35)
Continuity mistake: In the library scene Indy discovers the "X" high up on the balcony. The X is green with a grey background. When he breaks the tile to find the tomb the X has become a faint outline on the floor. (00:27:40 - 00:28:45)
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.
Plot hole: When the group is walking through the jungle for the 2nd time, they have nothing more than their backpacks and a horse to accompany them. Suddenly we see them rowing down a river on a boat and raft. After making peace with the savages, when they have to let a group member go to get medical help, they have been washed ashore as they have been traveling on a single raft since the canoe was damaged by spear attack. How is it that they had a horse and an Indian guide to send away with their injured man? (01:16:55)
Plot hole: During the later parts of this movie there is much talk about 'continental displacement' and this appears to be happening in the film. The Earth's crust is falling apart because of the heating of the inner core, and all the cities seems to be falling apart since the ground can no longer hold them. When our cast finds themselves surprised to be already over China when they figured to be over the ocean, it is explained that Asia has actually moved from where it was. If this phenomenon is taking place globally, how come the monks in China don't seem to have been disturbed at all? In fact the bell the monk rings as the ocean approaches hasn't even been shaken. The arks are built in between the mountains, but the mountains are apparently fine. Shouldn't they be falling like the rest of the crust?
Other mistake: When the Japanese planes take off for Pearl Harbor, some of the 3 man torpedo planes only have a pilot.
Continuity mistake: After being chased by soldiers after talking to his uncle, Dastan gets into a swordfight with Garsiv. As soon as it starts, Garsiv hits a pillar with his weapon knocking a significantly large chunk and a another smaller chunk out of it. In the immediate shot, the size and locations of the two chunks differ.
Plot hole: There are six metal bars mounted around the circumference of the water wheel's axle. In the wheel's interior, when Jack frees himself he lands on his feet, begins to run and promptly hits his head on one of those axle bars, then falls out. Moments later, when Jack returns and runs in the wheel, he is shorter (way more than a foot) than all six spinning axle bars, which would make that previous shot impossible, however humorous it is. (01:52:40 - 01:53:55)
Revealing mistake: When the team descends to the bottom of a hole and one female member is first wounded and then dies. After checking her pulse, the others pronounce her dead and begin moving out. As the last one is leaving, the "dead" actress lifts her head up off the ground and looks left. (01:13:10)
Continuity mistake: When the two female characters enter the fancy hotel room, they make a point to say they will only be there for a couple of minutes. It is daylight when they go in. The visit is cut short (the one that's supposed to be a few minutes long) because of a gun battle in which one of the women dies and the other escapes. The escaped one gets out through the roof into an evening's sky. There's still light visible, but for a visit that lasts all of 4 minutes, it's far too quick a change. (00:23:00)
Plot hole: Harry tells Doc Ock that in order to find Spider-Man he must find Peter first. Doc Ock finds Peter with Mary Jane in the cafe and throws a car through the window straight at them, then later throws Peter against a brick wall. Any normal person would've been killed instantly (or very badly injured), and Doc Ock doesn't yet know that Peter is Spider-Man. Given that Peter is his only lead on Spider-Man, it makes no sense that Doc Ock would try to kill him.
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.