Continuity mistake: Becker is the last to go through the hatch into the NEB bunker, but when the camera switches to the view inside the bunker, Becker is seen already on the walkway while the others are still climbing down the ladder.
Revealing mistake: Near the end of the film Willy jumps on a barrier in the water, causing it to break. During that scene its clear that the orca has been pasted into the background as the outline is too sharp.
Continuity mistake: When Max is running out of the school after successfully becoming cool. We see his friend with the orange mohawk at least twice. Once hanging from a statue, and another where he's reaching out from a school bus. These two shots are really close together so there is no way that he could have moved that quick.
Continuity mistake: When Angus and Yellow reach the lake, Angus's face is tore up pretty bad, but after they cross the lake and go to the building on top of the mountain his face is almost completely free of any injuries.
Factual error: In the movie, Wild Bill has a shootout with the bad guys in the stables. He is holding two colt revolvers, each having the capability of holding six rounds each. However as a safety precaution, only five rounds were loaded in the revolver with the hammer resting on an empty chamber as a safety. Therefore, he could only have ten rounds total from the two colt revolvers. He fired far more than ten rounds without reloading.
Continuity mistake: When the cruise ship is overrun by pirates, one of them being pursued by Indy jumps down the stairs fine, but when Indy does it he fails and his hat comes off to the left of the staircase far from his reach. When the shot changes its back on his head.
Factual error: Calamity Jane was not Pecos Bills love interest. According to legend Pecos Bill was married to Slue Foot Sue another tall tale. Whereas Calamity Jane was an actual historic figure.