Continuity mistake: When the camera shows the back of the truck, there are two soldiers on each side of the truck, plus the sergeant inside it. Following that, there were seven soldiers and one of them fell off the truck – there's a missing soldier in the scene. (01:25:50)
Continuity mistake: In the submarine dock of Geheimhaven, Captain Mohler is a man with dark hair in his mid or late thirties. But during the procession, he seems to be much older, with grey hair.
Continuity mistake: When the Nazis are aboard the Bantu Wind, in the full scene of the ship deck, Toht stands behind Belloq. But, after Marion tries to hit Dietrich, the camera focuses on Belloq, then on Dietrich again. Toht is not seen anymore on the deck.
Continuity mistake: When the Nazis are loading the Ark in the truck, you can spot Toht next to the left side of the truck, watching the scene. A few seconds later, he walks out of scene, apparently going to the car. However, when Belloq and Dietrich walk to the car and Belloq shouts "Let's go!", Toht has disappeared. (01:21:45)
Continuity mistake: When Dietrich, Gobler, and Belloq arrive next to the destroyed Flying Wing, Gobler is on the left of Dietrich and Belloq on the right. In the next shot, they have changed places. (01:20:58)
Other mistake: The Angel of Death attacks the altar and Toht and Dietrich scream because of its revelation, but Belloq, for some reason, doesn't seem to see it. Just before the fire column rises, he's still calm. (01:47:10)
Suggested correction: If you don't know the reason, perhaps you should ask a question instead of assuming it is a mistake. Belloq studied the ark and probably better predicted what might come out of the ark. He is also looking directly into the ark and is mesmerized by what he is seeing, until eventually he does scream before his head explodes. The other two are terrified at seeing the apparitions.
Actually, it's pretty impossible that Belloq studied the Ark. If he knew what would come out of it, he literally committed suicide by opening and watching the Ark open, which doesn't make sense. He believed during the whole movie that the Ark contained the Ten Commandments tablets, not some kind of ghastly things.
He didn't know what would come out, but it doesn't mean that he, like Indy, expected just 2 stone tablets. He expected power, for him mostly.
Factual error: The captain of the Bantu Wind, Katanga, wears a hat that originated from the Yugoslav People's Navy. But the Yugoslav Navy wasn't formed until 1945, 9 years after this movie takes place.
Factual error: During the fight scene at the German flying wing, the pilot ducks into the plane and pulls out a pistol and cocks it. The pistol is a P38 9mm semi-auto that the Germans did not issue until 1938, two years later.
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.
Character mistake: When the crew of the German U-boat boards Katanga's ship, the submarine moves in a position perpendicular to the ship's bow as if to block its path. In reality, this would have been a pretty stupid move by the German captain, as Katanga could have rammed the submarine easily. Any kind of damage to the hull, especially ramming damage (even from small ships), would have been catastrophic to the submarine. It makes no sense to make a manoeuvre like this.
Continuity mistake: As Indy and Marion are starting to run from the plane, you can see the yellow wheel chocks are back in place under the plane's tires.
Factual error: When Indy flies to Nepal, there is a scene of the sea plane taking off with the Golden Gate Bridge in the background. The movie is set in 1936, and the bridge wasn't completed until 1937, with pictures from December 1936 showing large gaps still in the deck that do not appear in the movie. (00:23:00)
Other mistake: At the beginning of movie when Indy is about to steal the gold idol, the camera does a close-up of it. The idol has been in a decaying temple for hundreds of years. but it appears shiny and new, as though just placed there. You'd expect the idol to at least be dusty or covered in jungle debris.
Other mistake: When Indy and Marion are sealed in the well of souls, they are completely cut off from the outside world. As such, other than the torches, it should be pitch black, but it is surprisingly well lit in there.
Factual error: There's absolutely no way Sallah and Indy would be able to lift that 'lid' (for lack of a better word) off the ark. That thing is solid rock and would weigh close to a metric ton - and none of them look like professional deadlifters to me.
Factual error: When Indy is attempting to steal the Ark when driving the truck, one of the soldiers shoots him in the arm. Then another German punches him repeatedly in the same arm, causing Indy great pain and injury. After suffering a wound like that there's no way he'd be able to move that arm, let alone raise it above his head. But the next day after the boat is stopped by the sub, Indy jumps into the water and swims to the sub without any problems.
Other mistake: One of the soldiers at the table Sallah and Indy walk next to, is only pretending to eat with his spoon. (00:54:53)
Continuity mistake: In the chapel, before Indy turns the chalkboard over to explain the staff of Ra and the medallion to the G-men, the chalkboard goes back and forth from tilting forward to tilting backward a few times.
Continuity mistake: When Toht frees Marion, Dietrich enters the tent, and a few seconds later, Gobler does the same. In the next shot, Gobler enters first, and Dietrich second. (01:07:52)
Continuity mistake: When Belloq and the Germans are at the Well of the Souls, a top-down view shot when Indy yells, "Why don't you come on down here and I'll show you!" shows Belloq and a German soldier kneeling down to the left of him, also looking down into the hole. But, the side view shots show only Belloq standing near the opening.