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.
Continuity mistake: The 109s that are animated are shaped like the original German fuel injected ones. The shots where it's a real plane show the modified one with a RR Merlin engine that gives it a weird square nose.
Continuity mistake: As Sallah pulls Dr. Jones senior off the tread of the tank, Indy lets go of his whip and turns towards the German colonel and they continue fighting face-to-face. You can see that Indy punches the colonel so that he loses his balance and stumbles backwards. A split second later, the colonel is standing behind Jones with his arm around Indy's neck. They did not have nearly enough time to so radically change positions. (01:32:15)
Continuity mistake: When Indiana pushes the Nazi colonel out of an open window, if you look carefully, the colonel fell a few metres out of the zeppelin before landing on a pile of suitcases, but when the colonel looks up, the zeppelin is several hundred metres above him, in too short a time to ascend that much.
Continuity mistake: When Indy meets Hitler, there is a shot over Indy's shoulder that shows his lips are slightly parted (relaxed). Cut to Indy's face and he closes his mouth tightly. In the very next shot, with no elapsed time, we see from Indy's shoulder again that Indy's mouth is relaxed as before. (01:10:15)
Continuity mistake: Onboard the ship at the end of the prologue, after Indy grabs the cross before it falls over the side, the guy in the white suit climbing up the steps. He's only reaching the top as the shot changes. In the next shot, he's already a few steps away from the top of the steps, telling his men to stop Indy.
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 the Hatay soldier is decapitated in an attempt to navigate the temple's defences, his head rolls along the ground and Elsa turns her head around and looks over her shoulder. In the next shot, she has now turned her full body around, and in the shot after that, she is looking over her shoulder again.
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)
Continuity mistake: While Henry and Marcus are being held inside the tank, Indiana rides in circles and baits the tank to ram into one of the cars. In a following shot when we see Vogel walking toward the window inside the tank it's a flipped shot, note everything is backwards. Then two shots later, when Vogel shouts "quick" in German it's another flipped shot, and about five shots after that again flipped. (01:29:30)