Continuity mistake: As Indy and Satipo enter the temple, When Indy says to Satipo "stop" he is holding the whip in his right hand, yet when Indy says "stay out of the light" the whip is in his left hand. (00:05:10)
Continuity mistake: When Indy is climbing into the map room, he throws the staff of Ra down the hole, yet when he climbs down, it's resting perfectly against the wall, as if someone had placed it there. (00:50:40)
Continuity mistake: In the scene where Sallah and Jones are in the Well of Souls where they are putting the sticks in the Ark to left it up. Notice Sallah stick, when he first puts it in, on the stick are no tassels. But when they both left at the same time Sallah same stick that he put in has tassels on it.
Continuity mistake: The fight scene in Marion's bar clearly shows Indy using an automatic pistol to shoot at the bad guys. You can see the slide lock open when he runs out of ammo. But when the scene switches he is holding a revolver. Then when the huge guy is strangling Indy and the German says, "Shoot them, shoot them both." Indy is once again holding an automatic.
Continuity mistake: As Indiana writes "Neolithic" on the blackboard in his classroom at the beginning of the movie, he stops and checks to see if he's spelling it right, then finishes writing it. Later shots of the board reveal the same word on the board, only either the handwriting is different or the actual structure of the word has changed.
Continuity mistake: During the scene where Indy and Marcus are with the Army intelligence agents, watch the agent who is wearing the light blue suit - at the moment when Marcus refers to a secret chamber, the agent in the blue suit has his right hand resting on top the chair that he is sitting on, but in the next shot when he replies "secret chamber" his right hand is now on his face. (00:17:55)
Audio problem: Watch and listen when Marion is being held prisoner in Nepal by one of the thugs. As he seizes her, she's grunting in strain/pain. We can see this in the first, frontal shot of them. However, in the following side shot (from slightly behind Marion as Toht walks over with the heated poker), Marion's mouth is completely still and almost shut, yet her sounds continue (and these sounds would have to be made with wide-spread lips).
Continuity mistake: When Indy is packing his suitcase to go to Nepal, he picks up a gun that is wrapped in a piece of cloth, he tosses the gun with his left hand into his right hand and begins to unwrap the gun from the cloth by raising his right hand, so that the gun will fall into his left hand, but the gun ends up falling into Indy's right hand instead of his left hand. (00:22:10)
Continuity mistake: In the map room, Indy pulls out a notebook and takes off the elastic band. The elastic goes flying away. Moments later he closes the book and the elastic is in his hand. Also, the elastic starts off being pink (the one that flies off), then blue (the one that he puts back onto the book) and ends as tan coloured when he puts the book back in his pocket.
Revealing mistake: When Indy is fighting the big German at the plane, if you look at the wheels when the plane is turning around, you can see a chain and sprocket assembly that is driving the wheel to actually turn the plane. (01:18:55)
Plot hole: Indy stows away on the Nazi sub on the way to the secret Nazi base somewhere near Greece. Where did he stay all that time? Inside? On a VII-Class boat, there's barely enough room for the regular crew, and hardly any places to hide. Also, everybody knows everybody, so no passing yourself off as "the new guy." Outside then maybe? Well, the boat did dive, it's in the dialog, and while on the surface, German U-boats always had a bridge watch on the tower, so no luck there either. Note that by all accounts I could find, German submarines were required to always post a bridge watch, if only because otherwise they would be running essentially blind. It's not like the helmsman's station in the tower had any windows.
Factual error: When Indiana Jones ambushes the Nazis with the Ark, he threatens them with an anti-tank rocket. This is set in 1936, and anti-tank rockets weren't developed until the American M1 in 1942. The Germans immediately copied it from captured weapons and made their own much larger version known as the Panzerschreck, then Panzerfaust. The Russian RPG which Indy is holding was developed from the Panzerfaust in 1949. (00:41:55)
Continuity mistake: When Indy is in the map room, he blows sand away from a hole and a bunch of hieroglyphics, but in the next shot, there's sand scattered all over the stone he just finished clearing away. (00:52:10)
Continuity mistake: When Indy goes through the windscreen in the scene where he is fighting the balding blonde German, the stunt double playing the German has a full head of brown hair. (01:27:10)