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.
Sacha
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.
Sacha 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.
Sacha Continuity mistake: While Indy descends the Well of Souls the glowing logs underneath keep changing positions.
Sacha 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.
Sacha Continuity mistake: After the guy with the patch and the monkey greets the Nazis, Marion and Indy are seen walking through town, passing by an arched door. A frame later, from a different angle, they are passing by again and the amount of people around has increased.
Sacha Continuity mistake: In front of the idol, Indy shows Satipo the trap on the floor. Satipo's head position is different in all 3 shots in barely 2 seconds: First he's looking downwards, then straight, then his head is turned sideways, and then back to straight. (00:08:20)
Sacha 
Continuity mistake: In the marketplace standoff between Indy and his would-be attacker, in shots from behind Indy, he's facing one way, but in frontwards shots, he's facing a different way and when it cuts back to behind him, he's facing the other way again.
Clerk13
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 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.