Continuity mistake: During the truck chase, as Indy is fighting with the German driver, they knock over some scaffolding and a man drops down in front of the windshield. None of the workers on the scaffolding landed on the truck, much less the front of it. So, he shouldn't have been there.
Continuity mistake: In Indy's class at the beginning, the girl that lowers her eye lids to show the phrase "Love you", is looking in a totally different direction than the people behind her. They're all supposed to be looking at him, but the girls behind her are looking to their right while she is looking straight. They can't be daydreaming because they're all smiling and look infatuated. (00:13:58)
Continuity mistake: When Marcus enters the classroom he leans up against a wall and there are 2 girls in the front row next to him. When the bell rings, the girls are the first two students to leave the classroom. Seconds later when Indy looks over to Marcus the same two girls are just getting up from their desks.
Continuity mistake: Indy and a Nazi soldier are fighting in the cab of the truck when they come to a place where a stone building is being built. As the truck is driving into the scaffolding, several rocks come down and hit the truck and remove the rack from the top. Moments later the rack is back in place. (02:50:00 - 03:01:00)
Continuity mistake: When Indiana is confronted by the Cairo swordsman, he already has his left shoulder pointing towards his opponent in the shot where the crowd scatters. But in the following shot, where the swordsman is first seen, Indiana has his right shoulder pointing forward and is just turning around to his left side. (00:40:14)
Continuity mistake: When Indy is driving the truck, chasing Belloq and his Nazi cohorts, the last Nazi guarding the Ark of the Covenant climbs to the driver's side of the truck and kicks Indy away from the steering wheel. The first time he punches Indy in the arm, Indy's blood is on his fist. However, the second time he punches Indy in the same spot, there is no blood on his fist.
Visible crew/equipment: As the bad guys are leaving the dig site for Cairo, there is a shot of the black vehicle (lead car) looking right at the driver. On the bottom of the shot is a shadow of film equipment that shouldn't be there. The shot lingers, so the shadow is very visible. (01:22:50)
Other mistake: In the bar shootout, a man is shot in the head. The bullet hits him in his hat right in the middle of his forehead, and then his hat falls off. But we then see a close-up of his face, and there's no bullet wound in his forehead or anywhere else.
Continuity mistake: When chasing Indy in the truck that he has driven into a fruit market, the Germans in their car are surrounded by fruit sellers. One gives a German soldier a melon, who promptly throws it to the ground on the left side of the car. When the car pulls away, the broken melon lies on the right side.