
Continuity mistake: While the Ark is killing the soldiers, the cameraman is hit twice, as the first hit is shown in the first wide shot of the dying soldiers and the second when the camera focuses on the cameraman. Also, during the second hit, a beam passes through the camera and strikes the cameraman in the face, although he remains standing. In the next shot, the cameraman's body is suddenly on the ground and the beam that had killed him disappears.
Audio problem: When the camera focuses on Belloq as he looks into the Ark, Toht's screams are inaudible, despite being right next to the Frenchman. Only when the shot changes to show Toht his screams can be heard.

Continuity mistake: As Gobler's jeep is returning to the road after being hit by Indy, Gobler's goggles move from his eyes to his cap between shots.

Continuity mistake: When Dietrich and Toht look at the ghosts that pass behind them, the column of mist that is coming out of the Ark disappears.
Continuity mistake: Between the shots of Indy dressing as a Nazi and Captain Mohler reporting to Belloq and Dietrich, the Wurrfler appears to have advanced several inches forward (taking as reference the background behind the submarine, Mohler's location, and the fact that Belloq turns his head to the left to look at the Captain).
Continuity mistake: As Dietrich, Toht, Belloq and Marion board the Wurrfler, a naval officer descends the ladder and turns, his back to the ladder. In the next shot, he is facing the ladder.
Continuity mistake: The Angel of Death, judging from the position of the lid of the Ark (the two angels can be seen below the ghost), is located just above Dietrich's head. However, Toht screams as if it were right in front of him and Dietrich as if it were in front of Belloq (judging by their looks).

Continuity mistake: The distance between Otto and the Nepalese changes between shots, just as Toht begins saying "Surely he told you..."

Continuity mistake: In the shot after Belloq's death, the generator and the rock Indy and Marion are on disappear.

Continuity mistake: As Dietrich and Gobler come into the tent, Toht's leather case can be seen already opened. In the next shot, the case is suddenly closed.
Audio problem: After Dietrich pours liquor for himself, he speaks to Belloq. One of the words of his phrase (probably monsieur or Belloq) was cut from the audio as Dietrich's lips still move but nothing can be heard.

Visible crew/equipment: During Marion and Belloq's beverage contest, a round klieg lamp's blue light stands behind Belloq, which sometimes changes its intensity. Also, when Marion grabs the knife, behind her a moving light can be seen (like a helicopter's light), which disappears a few seconds later. This light also appears for a few seconds when Toht frees Marion's arm.

Continuity mistake: When Indy abruptly brakes the truck and the Ark box slides backwards, the poles on either side of the box disappear for the rest of the chase.
Audio problem: Just before Belloq opens the staff car's door, Paul Freeman's voice can be heard saying "Let's get out of here" but Belloq's lips don't move.
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).
Answer: I also remember this scene. After the ark is sealed, the camera performs a close up of the side of the crate. The stamp reads "Top Secret Army Intel 9906753 Do Not Open" This stamp is burned off just like the swastika is in the scene on the submarine, because in the eyes of God, no nation is holy or worthy enough to claim ownership of the ark. However, this final scene was cut (the burning of the stamp) from the film for a variety of unclear reasons. While it was in theaters, this scene was not included on the DVD version.
Add me to this. We saw the movie in a "pre release" version in Orlando Florida. No advance warning of the movie. We went to see another flick and at the end were "invited" to see this if we were willing to critique it afterwards. This scene was included. I also always wondered why the change.
I also remember seeing this mysterious 'burning' of the logo, most likely it was on a VHS copy of this movie. Yes, it did exist.
I saw it in former Czechoslovakia in the second half of 80's in cinema (west movies came to the east countries' cinemas years later). And I thought it was a great joke that burning out the swastika wasn't just because the Nazis are bad but because nobody is great enough to own the arc. Then after the Velvet revolution I saw the film again on TV (beginning of 90's) and said everyone around: watch it until the end, wait on the post-credit scene, there will be a surprise.
And there was a surprise. The scene was cut off! I was angry on the TV they didn't show the scene. I cannot be influenced by internet discussion or urban legend. The internet didn't exist yet.
I saw it in Portland, Oregon, and was so impressed with the message it carried, that I told friends and we went several times just to see it. Funny thing was when I mentioned it a few years ago, many people said I was a LIAR that it never happened. I could not convince anyone. It was removed because it wasn't Politically Correct. USA is a force for good, God would not burn off AMERICAN TEXT! BUT WE DID SEE IT. Thanks to our Australian eye witness, we know we did not imagine it.