Continuity mistake: When the temple collapses, Indy is holding the idol with his right hand against his chest, and the left hand free and arm extended. A frame later, both arms are extended and holding the idol.
Continuity mistake: When Indy is listening to the one Army agent he is in the process of putting his right hand into his pocket. In the next shot the hand is back on the leather case. (00:16:46)
Continuity mistake: When the Cairo Henchman pulls the knife on Marion, the blade edge changes position from down to up to down again.
Revealing mistake: During the big car chase where Indy follows the ark, he comes down a hill on a horse to get into the truck. You can tell the ground has already been disturbed by the horse from previous takes.
Revealing mistake: After the German is chopped up in the propeller and the plane explodes, you can the blasting cord exploding along the path to the explosion.
Continuity mistake: When Indy sits down in the seat of the plane look behind him, there is nobody holding a Life magazine or fitting the description of the man later shown watching him from the other seat.
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: As the big German engages Indy in the fight, Marion is removing the chocks from one of the wheels. In the wide shot you don't see her at all, even climbing the plane to knock out of the pilot.
Other mistake: After Indy shoots the driver of the truck that Marion is supposedly in, the camera looks at the driver's bloody hand falling limp. In the shot of the truck tipping over, you see the stunt driver working the wheel.

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: While escaping from the boulder, right before the spiderweb scene, Indy runs facing forward and makes a right turn. A shot later from a wide angle he is facing backwards.
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: When Indiana is thrown through the windshield of the truck during the truck chase scene, there is another man in the driver's seat leaning toward the door, driving the truck with dark hair. This is noticeable just as the glass is broken.
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)
Continuity mistake: Arnold holds a hot stick of metal to Marion's face in her bar, threatening her. In the opposite angle, the metal is nowhere to be seen when it should be right next to her face. Cut back to the other angle and we see it again.
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.
Suggested correction: Wound easily could be on a hairy part of the head.
Even in a close up a bullet wound would still be visible due to the size of the wound.
Continuity mistake: In the bar shootout, a man is shot in the head, and as Marion screams in shock she's holding onto the table. In the very next shot her hand is much lower.