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 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.

Continuity mistake: As the ghosts dance around the pole to which Indy and Marion are tied, large clouds can be seen in the sky behind them. However, after a ghost circles Dietrich and passes in front of the camera, it can be seen in the background that the clouds behind Indy and Marion have disappeared.

Continuity mistake: As the ghosts dance around Dietrich, Belloq, and Toht, the Frenchman slowly looks up as the column of mist ascends upwards from the Ark, almost looking straight ahead. In the next shot, Belloq is looking down again; the shape of the mist has changed, and the column of mist is now moving to the right.

Continuity mistake: As the truck pulls up next to the Command Tent, four soldiers lift the Ark's box and a fifth soldier, positioned between the two wooden posts of the Ark's box and to Gobler's right, picks up the sticks that Indy and Sallah had used. In the next shot, that soldier is now to the left of Gobler and the Ark's box. (01:21:40)

Continuity mistake: The distance between Otto and the Nepalese changes between shots, just as Toht begins saying "Surely he told you..."
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.
Suggested correction: This is not true. Dennis Muren enters just before Indy and sits down. The camera focuses on Indy, giving Muren enough time to grab the magazine and cover his face.
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)

Continuity mistake: The amount of moss behind the idol increases between shots.
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.
Suggested correction: This entry is incorrect; the poker is always on screen, it never disappears.
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.