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 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: In the beginning where Indy is young, he fights some guys on that zoo train. When he's on the crate with the rhino in it, the background changes in each shot. Once there are trees behind and a split of a second later there are rocks, once there's a cliff and once a plain, and it all changes in splits of seconds as they change shots. (00:07:25)
Visible crew/equipment: When Indiana and the Protector of the Grail are fighting in the boat that is about to be chewed up by the giant screw/propeller, when the angle changes to the top point of view, you can see the rope pulling the front of the boat around to position the rear for destruction... (00:39:10)
Continuity mistake: When the Nazi Colonel discovers Henry Jones sen. aboard the zeppelin, Indy asks him for his flight ticket. In the first shot, Indy is standing right beside the colonel (the camera is behind the colonel and Indy comes in from the right), in the subsequent shot, Indy is standing behind the colonel.
Continuity mistake: When Indy gives his father water from the grail to drink, the grail glows from inside, and the gold inside it is bright and even. But when Indy pours water over the wound, the grail is dark inside and there are dark patches in the gold. Obviously, they had to take the light that made the grail glow out so it wouldn't be seen when Indy pours the water over his father.
Other mistake: While Indy and Henry are aboard the zeppelin Indy tosses Vogel out the lounge window, and when Vogel shouts up to the departing airship, in the next exterior shot we see the zeppelin airborne against a scenic view. Later, when Indy realises the zeppelin is turning around it cuts to another exterior shot of the airship, and the scenic view is identical to the earlier shot, only it's been flipped. The images of the zeppelin facing two different directions were composited onto the same scenic background.
Continuity mistake: During the temple quake sequence towards the end of the film, Elsa fails to maintain her grip on the rising earth and falls onto tilted ground, sliding towards the chasm. At this point, Sallah is kneeling on the ground, but in the very next shot, he is now grabbing hold of Henry.
Continuity mistake: When Sallah rides up to the tank to rescue Henry we see Indy toss the whip over the side of the tank, but after the tank falls over the cliff, when Indy climbs back up then walks over to stand between Henry and Sallah the whip is coiled and back in its place, hanging from his belt. Even Indy can't do that. (01:36:00 - 01:37:40)
Visible crew/equipment: When Indy tries to reach the Grail his father convinces him to "Let it go" and Henry pulls his son to safety, then in the next wideshot of Indy, Henry, Sallah, and Marcus a crewmember wearing a short sleeved, white shirt and blue pants can be seen at the right side of the screen, just before it cuts to Henry's closeup. This crewmember can be seen again after the closeup of the knight. (01:57:45)
Visible crew/equipment: After Young Indy locks the two treasure hunters in the reptile train car he pulls a snake out of his shirt, and just as the third young treasure hunter tackles Indy we can see a crewmember's arm and equipment at the left side of the screen, before it cuts to the long shot. (00:07:00)
Other mistake: After Young Indy runs out of the cave with the Cross of Coronado, when he whistles for his horse and jumps down, note the horse's facial marking and leg marking. When Indy mounts the horse it's a different horse, note its markings, and as he rides toward the circus train the horse has changed again. (00:04:55)