Continuity mistake: In the boat chase, when the bad guys are using machine guns, in one shot we see Indy's boat in the middle of the canal. In the next shot (close-up) they are very close to a large pile of dirt (or wood chips) and in the next (wide) shot they are in the middle of the canal again.
Continuity mistake: During the boat chase/fight in Venice, the rear of Indy's boat gets shot up and starts smoking and spouting flames and the engine starts chopping. He leaps onto the pursuing boat, fights until that boat is destroyed in the rotors, then leaps with the Grail protector back onto his original boat with Elsa. The boat is now running perfectly. (00:38:50 - 00:39:55)
Continuity mistake: When Indy and his father are being pursued by German soldiers on bikes, right after they break through the barrier, the barrier guard comes out of his post and waves the pursuing German soldiers to slow down in the background. In the next shot he's no longer there, and the barrier's quite far away, then in the following shot he's back, and Indy's not so far from the barrier again. (01:04:35)
Continuity mistake: In the catacombs underneath the library, when he find the "X" on the wall, he is shown ramming the wall twice to break through. The first time he rams it, however, the wall looks as if he had already had a few goes already. (00:31:55)
Continuity mistake: When Indy and the protector of the Grail are in the boat about to be destroyed by the rotors, there are panels on the top of the boat that pop up and are destroyed when the boat is moving backwards into the rotors. In the next shot, they are intact, then in the next shot, they are destroyed again. (00:39:20)
Continuity mistake: When Indy comes face-to-face with Hitler he hands over Henry's diary with its black elastic around the back cover, but in the closeup as the signature is being signed the elastic is around the front cover, then it's around the back cover again when Indy takes the diary back.
Continuity mistake: When the Nazi is strangling Indy with the chain, Indy looks down into the porthole of the tank and yells, "Dad!" Before he throws the gun down into the tank Indy's hat comes loose, but when the next shot is back on Indy, and he yells, "Dad! Dad, get out!" now his hat is back to normal.
Continuity mistake: When we first see the knight guarding the Grail, his cloak is tied off with a braided rope, which hangs down on his right side. It stays this way until he says "You have chosen wisely," where the rope has somehow shifted to his left side. The rope goes back to normal when the knight waves goodbye at the end of the movie. (01:49:10 - 01:54:05)
Continuity mistake: When the white robed men ambush the Nazis just after they blow up Salah's car, there's a shot over a Nazi's shoulder as he fires at one of the white robed guys running up a hill. The Nazi's machine gun is held straight out and doesn't move but the dust that flies from the squibs suggest that he fired as he moved the gun right to left which he did not do. The odd thing is that AFTER the squibs go off, the Nazi turns his gun to the left. (01:25:55)
Continuity mistake: When Indy takes four horses before battling with the tank, three are black and one is bay (brown with black legs, mane and tail). Sallah is riding a chestnut. When they ride to the Grail Temple, there are two black horses and two chestnuts. Where did the second chestnut come from? (01:28:00 - 01:39:25)