
Continuity mistake: In the market chase scene Marion is confronted by a guy with a knife. In some shots the sharp edge is facing upwards, in others it's downwards. (00:39:10)

Revealing 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)
Continuity mistake: During the middle of the bar fight scene, Indy was slammed on the counter and whispered to the girl, "Whisky". In the next shot she grabbed the bottle and handed it to Jones. The very next shot she hands him the bottle again. It happens very quick. Watch carefully. (00:32:05)

Continuity mistake: There's a shot of the plane at the beginning, taken from the front, looking down the length of the body, where there's no writing on the side. (00:11:45)
Suggested correction: On a good quality frame the number is visible quite clear. Not visible on a poor resolution frame.
Audio problem: When Marion and Belloq are getting ready to have a drink, as Belloq pours the wine you can hear the sound of the wine hitting ice, making a crackling sound, but there is no ice in the glasses. (01:04:40)

Continuity mistake: When Belloq grabs the machine gun, his left hand is on the trigger and his right hand on the gun cartridge as he turns round with his back to the camera, but in the next shot, his right hand is on the trigger and his left hand on the cartridge but in the next shot, his hands have changed position once more, this time left hand on the trigger and right hand on the cartridge. (01:42:55)

Continuity mistake: When Indy is chasing after the truck on horseback, he jumps off the horse and onto the truck, as he does this the horse begins to slow down and fall behind, but as Indy throws the German soldier in the passenger seat out of the truck the horse has disappeared, it could not have been hidden from view behind the truck, because the horse's shadow would have been visible. (01:23:30)
Audio problem: At the beginning of the film, one of the guides goes to shoot Indy with a gun, but as Indy uses the whip to defend himself, the gun bounces off a rock and goes into the water. As the gun hits the rock you hear the sound of the gun firing, but there is no sign of a flash from the barrel or any gun smoke. (00:03:10)
Factual error: Look to the right of the table lamp, there is a bottle of Myers Rum that has the modern plastic (silver/clear) cap and plastic pour spout. Not 1940s era. (01:33:10)
Factual error: When Marion is thrown into the pit of snakes and grabs the statue to prevent her fall, underneath her skirt she is wearing black spandex shorts. Shorts such as these did not exist in the 1930s time period of the film.

Continuity mistake: When Indy is running through the streets of Cairo looking for the men carrying Marion in a basket, the sweat stain on the back of his shirt shrinks and grows. (00:40:35)
Revealing mistake: When the German staff car comes into the market place to find no truck, watch as Dietrich hurls the melon - the Gestapo guy in the front is obviously a dummy for this one shot. (01:29:40)

Continuity mistake: Several times during the fight in and around the truck the bars around the top of the cab come off and are miraculously back on again. (01:24:05)
Revealing mistake: When Indy and Marion are being sealed up in the Well of Souls, You can plainly see Marion counting down (she is mouthing the numbers) to the cue for her to scream as the Well is sealed. (01:12:20)
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)
Factual error: The truck that turns over and blows up after Indy shoots the driver is a Mercedes Benz L701. It began production in 1944, and this movie is set in 1936, so the truck is not period correct. Also, the alleys are too narrow to allow this truck to turn a corner.
Revealing mistake: When Indy fights the driver of the Nazi truck, the windshield is smashed when Indy is thrown through it, but there is no wind. Look at the driver's hair, not one stirs from a breeze while driving a fast moving truck with no windshield? (01:27:30)
Revealing mistake: When Indy is running through the cave and finds the spy that took the artifact with spikes through him, he brushes up against the dummy and it shakes like rubber and the light bounces off it like rubber. (00:09:10)
Continuity mistake: When Indy is fighting the Nazis on the truck, one Nazi is thrown from the truck and is rolling the opposite direction of the truck. (01:23:30)

Continuity mistake: The position of the Top Secret sign and the whole text is put on the ark's box across vertically laid planks, with a wood crossbar on the right, which only the side panels have. 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.
Suggested correction: The other text and the different plank design could be on the base of the box or on the front wall (the wall opposite the man pushing the box), two walls we never see when the box is being pushed. In fact, at one point the camera passes next to a box that has two texts, one on a short wall and one on a long wall.