Continuity mistake: When young Indy fights a baddie, the rhino sticks his horn through the roof and the baddie is pushed to the right. When the angle changes he is falling on the opposite side.
Other mistake: In the fighter plane scene, their hats don't blow away.
Continuity mistake: When young Indy confronts the lion, the way the whip is rolled changes between shots. The second time a small loop appears.
Continuity mistake: During the rhino scene, the roof of the carriage swaps from dark grey to blue before the rhino's horn goes through the roof.
Continuity mistake: When young Indy falls on the rhino carriage, there's two banners whipping by each of his legs. When the angle changes (to an obvious chroma background) the banner on the right is gone.
Continuity mistake: When young Indy breaks the lion's carriage ceiling and falls inside, a wooden plank falls on his stomach. When the angle changes the plank is gone.
Continuity mistake: When the movie beings, the Boy Scouts at the end of the row dismount the horses, then the angle changes and they dismount the horses again.
Continuity mistake: While being chased by the plane, Dr. Jones faces backwards and cries "This is intolerable!", then faces forward and ducks. From the immediate wide angle he is still facing backwards.
Revealing mistake: When Marcus Brody is knocked out in the library, he is dragged away by two of the assailants. You can see the unconscious Brody give his right hand to the assailant.
Continuity mistake: When Indy and Elsa come up through the manhole their hair is sopping wet and messy. As they run to the boat their hair is magically styled and not sopping wet anymore.
Revealing mistake: When Walter Donovan is dying after drinking from the wrong cup, watch the over-the-shoulder shot where we see his hair grow long suddenly - for some reason, this shot was filmed in reverse, as the fire coming from the candles/torches behind Elsa is not burning upwards, but appears to be "sucking" back downwards.
Revealing mistake: In the shot of Elsa falling to her death into the misty chasm in the Temple, you can see that it is not Alison Doody but a stunt double.
Continuity mistake: During the escape from the Nazis the Jones boys pass through a boathouse and Indy sets a small boat loose with the engine running to distract them. When he releases the boat the motor (and boat) is turning to the starboard side (which would turn the boat straight back into the bank), but when the Nazis arrive, the boat is running perfectly straight down the river.
Factual error: When Indy and his father rotate into the control room, the eagle on the uniform of the woman who raises the alarm is on the wrong side, left instead of right.
Suggested correction: As it's an SS uniform, the eagle insignia should be on the upper left arm.
Continuity mistake: The blood on Indy's left ear disappears at the end of the film.
Continuity mistake: When Indy kisses Elsa in her room in Venice, you can see there is nothing on Elsa's left shoulder, but when the camera angle changes in the next shot, Indy now has his hand on her shoulder.
Continuity mistake: When Indy and his father take the car from the old man, you can see that viewed from behind Henry is the driver and Indy is next to him. In the next shot, they have changed positions and Indy is now driving the car.
Continuity mistake: When the brotherhood member aims his gun at Elsa whilst she is driving in the boat, Elsa ducks downwards to avoid the shot, but in the next angle, she is sitting upright.
Audio problem: Just after young Indy escapes the bandits on the train, he finds the magic cart and says "Magic" to himself, but a close look will show his mouth doesn't move with the line.
Continuity mistake: When Indy and Kazim are about to jump off from the chopped boat, the boat swaps from sinking to floating between frames.