Continuity mistake: In the scene where Indy is telling about the Staff of Ra, the background color of the blackboard changes between shots. It looks like there are some chalk residues (after the blackboard has been washed) in one of the shots, but not in the other.
Continuity mistake: The stone block Indy pushes out to create an opening which allows him and Marion to escape the Well Of Souls apparently rolls down the hill outside. We see it, in a following scene, laying about 15 feet away from the Well. But when Indy is fighting the big German guard near the airplane, one scene clearly shows the Well in the background and the dislodged stone is now laying on the hill only a few feet from the opening. (01:15:45 - 01:18:10)
Continuity mistake: When the government comes to see Indy at the University he is teaching, they enter the large room, I think it's a gymnasium. He puts the huge book on the table and one of the buckles comes undone. But when he goes to open the book to show the g-men a picture of the Ark he undoes both buckles. (00:15:30 - 00:19:30)
Continuity mistake: When Indy is being lowered into the map room, the exterior shot of the opening does not match the interior. From the outside, the wall around the opening is a lot thicker. The angle is also different. (00:50:55)
Continuity mistake: When Indy and the German driver crash through the villager's construction ladders the truck is missing the Mercedes-Benz hood ornament that appears in every other shot.
Continuity mistake: When Indy is trying to stop the truck that is supposedly carrying Marion in a basket, Indy shoots the driver as the truck heads towards a "dead end". The driver's foot hits the accelerator and the next shot opens up to a big open space where the truck tips over and explodes. The "dead end" has disappeared. (00:40:10)
Audio problem: When the monkey is crawling on Marion's head at Salah's place, the sound does not match Marion's mouth.
Revealing mistake: Just before Belloq says "beautiful", look carefully at the woman's ghost in the center of the screen. You can see one of the wires on her back that makes the stunt woman fly, a black line above her left shoulder.
Continuity mistake: When Sallah lowers Indy into the Map Room, from the outside Sallah is standing near the bottom of the hole, but from the inside the rope hangs from near the top. (00:50:55)
Continuity mistake: Just after Indiana (barely) escapes the tumbling boulder at the beginning of the movie, he leaps through a veil of spider webs, only to be held up by the native hunters and Belloq, who takes the idol from Indiana. Watch carefully - there is a thick strand of webs attached to the idol as Indy hands it to Belloq, but they disappear in the next shot as Belloq hefts the idol and holds it up in the air.
Factual error: The German submarine that Indy stows away on has the number 26 on its side. The U-26 was a Type IA U-boat (it came into service in 1936 and was sunk in 1940), but the sub in the movie seems to be a Type VIIB or VIIC. It's true that the two types looked fairly similar, but they were different classes of U-boat.
Continuity mistake: The 'Top Secret' sign is put on the crate across vertically laid planks. A shot later the sign appears slanted across horizontally laid planks. Though it could be argued that there could be a second sign on the opposite side with horizontal planks, when the warehouse guy turns left to store the crate, we get a glimpse of the left side and it's not painted.
Continuity mistake: Sallah and Indy are peering into the well of souls. Sallah is to the right of Indy. Indy then drops the torch into the well, and when the camera comes back up, Sallah is on the left of Indy. (01:00:00 - 01:00:45)
Suggested correction: Indy and Sallah spent several seconds off-camera, enough to move around the hole and switch places.
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.
Factual error: The interior of the German U-boat is completely different from the real interior of a Type VII U-boat, which is correctly shown in movies like 'Das Boot' or 'U-571'. For example, the ladder from the conning tower faces a different direction, the map table is too big and on the wrong side, the valves for submerging are on the side of the control room and not at its front and stern, depth gauges are too big...etc. All interiors were standardized, so it could not have been an individual build.
Continuity mistake: During the shooting at the bar, Marion covers her ears to muffle the sound, but a frame later they are around the wall in front.
Audio problem: In the bar, when the man is shot in the face and burns alive he screams in pain, but he never opens his mouth.
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.