Audio problem: After Dietrich says "And Gobler, I want plenty of protection", a German voice can be heard saying "Jawohl, Herr Oberst", just before the tower behind Belloq explodes. This voice sounds extremely close to the three villains, although neither of them have spoken, and there are no more people next to Dietrich.
Continuity mistake: During the procession, after Indy hides behind the box, Captain Mohler can be seen walking with the soldiers behind the Ark. In the next shot, he's walking in front of the Ark.
Continuity mistake: In the first scene of the procession, the Nazis are walking in a straight line along a path. In the next shot, they are now going around a curve.
Continuity mistake: When Marion gets off the submarine, there are two soldiers behind her. In the next shot, one of the soldiers has disappeared.
Continuity mistake: When the Wurffler arrives to Geheimhaven dock, six soldiers and an officer are running towards the submarine. In the next shot, the seven men have disappeared.
Visible crew/equipment: Just before the shooting starts at The Raven, you can see that Otto's shadow movements do not match the German's movements. Also, when Marion fights with Toht, behind her you can see the shadow of a man with short hair and no hat moving to the left (Indy still has his hat on during this scene).
Continuity mistake: During the procession scene, in the shot before Toht takes off his hat, about twenty soldiers can be seen walking. After Indy leaves the procession and hides behind a box, in the next shot, there appear to be twice as many soldiers as in the first scene. Just before Indy shouts "Hello!", the quantity has returned to twenty.
Continuity mistake: After the kliegs behind Dietrich, Belloq, and Toht explode, the Ark's energy begins to destroy the soldiers' guns and the kliegs next to them. In some shots, the kliegs on the altar are still working.
Character mistake: In the original Latin Spanish dubbing, Dietrich calls Gobler "Glober" while walking next to the destroyed Flying Wing.
Continuity mistake: Just before Belloq says "It's beautiful!", there is a black machine (which is not the German camera or the generator) in the bottom middle of the screen, just below the approaching ghost. It is also visible when the Angel of Death is revealed. This machine disappears when the Ark begins to kill the soldiers.
Continuity mistake: After the kliegs and generator explode, there is a shot of Belloq and Toht on the altar. Belloq has the ivory rod in a vertical position. In the next shot, the rod is horizontal.
Continuity mistake: When Indy and his excavation team arrive at the true location of the Well of Souls, we can see that it is on a low hill, just a few meters from the Nazi excavations. However, when it gets dark, we can see that the excavations have disappeared from view and now the Well of Souls appears to be on a considerably high mountain (taking as a reference the illuminated camp on the right of the screen).
Continuity mistake: In Hangar 51, the size and position of the text in the Ark's box changes between shots.
This is not the same mistake as the one you listed. Yours speaks about the style of the box (that changes from vertical planks to horizontal planks). Mine speaks about the size and position of the text.
Mine is about the box and the text "The 'Top Secret' sign is put on the crate across vertically laid planks. A shot later the sign appears slanted." Yours is a duplicate.
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: 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 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 officer 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.
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.
Other mistake: In the opening scene Indiana is with horses and scouts. A few minutes later he is running for his life and in a few moments he's at a waiting plane. Why does he need scouts and horses for the cave is in walking distance from the plane and how did the scouts and horses get there?