Revealing mistake: When the thug with the blade sticking out his back is standing still, there is some kind of squared device on his back under his clothes, presumably to retract the fake blade to end the sequence.
Audio problem: In Marion's bar, she uses a burning log to knock one of the goons out. As his face changes, you hear "ow!" then he moans as he falls over. However, his mouth doesn't match any of the sounds.
Continuity mistake: When Indy is shot in the arm in the car, there's no blood on the windscreen at first, but in the very next shot there is.
Continuity mistake: When the guy at the start who betrayed Indy is shown stabbed by many spears, in the shot when Indy says "adios", he stays with him the entire shot. However, in the next shot, he's far away from him.
Continuity mistake: When seen from the outside the entry hole to the Map Room is quite vertical. The angle is different when seen from the inside. Further, the hole is so vertical that the sun wouldn't be high enough to shin through the hole at 9 am.
Continuity mistake: The amount of moss behind the idol increases between shots.
Continuity mistake: After the door to the Well of Souls is opened, Indy and Sallah take a sneak peek at the inside, immediately after, from a new angle, Indy sneaks in again.
Continuity mistake: The position of the dead monkey and the date next to him changes between the first and second angle.
Continuity mistake: The morning after Indy makes out with Marion, when he goes to check why the boat engines have stopped, the position of her hands, the wrinkles on the blanket and the dress behind the bed change positions between angles.
Continuity mistake: Indy walks to the hill where the ark is, holding a shovel that keeps facing different directions depending on the camera angle. Also, Indy holds it either by its black metal part or by the wooden stick. This all changes back and forth.
Audio problem: While Indy tries to escape from the Well of Souls a stick in his mouth falls on Marion, who starts to cry very loudly; however, her mouth doesn't move an inch.
Continuity mistake: In the map room, Indy places his brush facing a 9 o'clock direction. A frame later it faces a 6 o'clock.
Continuity mistake: In the map room, Indy brushes the sand off of a stone, leaving a clean horizontal trail. A frame later, in the close-up, the upper left part above the trail is suddenly clean.
Continuity mistake: When Belloq traps Indy in the Well of Souls the sky keeps swapping between a dim yellow dawn sky, and a brilliant morning blue sky.
Continuity mistake: While Indy descends the Well of Souls the glowing logs underneath keep changing positions.
Continuity mistake: In the bar, the Nazi plays with the fireplace and threatens Marion, who takes a cigarette to her lips. A frame later, her hand is in a totally different position.
Continuity mistake: After Marion's been thrown in the Well of Souls, a net and pair of sticks over the crate behind Belloq appear or disappear randomly between shots.
Continuity mistake: After the kids save Indy at the bar, he exits and there's a man on the right carrying a load on his shoulder. He appears and disappears randomly depending on the angle.
Continuity mistake: When Indy's crew is lifting the stone door to access the Well of Souls, big clouds of white smoke come out from every corner. A frame later, from a wider angle, they're gone.
Continuity mistake: About to grab the idol, Indy passes a stick over a pile of sand on the ground which has a leaf on the center. A frame later the leaf is on the left side.
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.