Continuity mistake: When the villains are following Indy through the caves, the old wooden bridge completely breaks and falls apart. However, when they make their escape across the same bridge, it's intact with only a couple of wooden slats broken.
Continuity mistake: After the Roman shipwreck, the Spanish flag on the dive boat goes from flapping vividly in the wind in one shot to then hanging limp in the next. This discrepancy is throughout all of the exterior dive boat scenes. This likely shows which clips were filmed on location and which were filmed in a studio. (01:09:40)
Continuity mistake: The license plate's number of Indy's Tuk Tuk changes from 4717 to 1132 in a few shots during the Tuk Tuk Chase.
Continuity mistake: While Indy is fighting Colonel Weber on the roof of the train, Basil is pointing a pistol at them, and his grip on the pistol changes from a two-handed grip to a wrist-stabilizing grip as the shots change.
Continuity mistake: At the start of the film, towards the end of the steam train roof battle, as Indy jumps from the train (200+ feet into the rocky shallow looking part of a river), it's still fairly dark in the early hours of the morning. As he surfaces seconds later, it's considerably brighter. Then, as he walks up the river bank, morning is well broken into much brighter light. Assuming the scene is set around March/April 1945, sunrise in the Alps is unlikely to occur so rapidly. (02:16:01 - 02:16:35)
Continuity mistake: Within the Roman shipwreck, Indy is grappling with his fear of snakes (eels) with his red flare; a torch light is briefly shone on his head from above. When the shot reverses to the diver at his rescue, she has no torch at all in sight. (01:11:12)
Continuity mistake: When Indy arrives in Tangier at Hotel Le Atlantique, it is evening. A party is going on in the hotel while the auction is being held. A discussion starts, and a fight breaks out. They go outside, and all of a sudden, it is daytime.
Continuity mistake: While on the boat, Helena does her 7 spades card trick. When she gives Indy a turn, you can see the bottom card is a black 2. When she fans them out, it changes to black king of clubs. Then, in the next shot, it changes to 8 of clubs. (01:16:00 - 01:17:00)
Suggested correction: Not necessarily a mistake. She could be changing those cards by sleight of hand, while moving the 7 of spades into position for the final force. The mistake was not using the 3 of clubs for it.
Continuity mistake: Klaber handcuffs Teddy and Hauke, then moves on. He is followed by Hauke, Teddy, and Gunther. In the next shot, Voller and the two unnamed Nazis have suddenly appeared behind Klaber, and Hauke (with Teddy) and Gunther have switched places. (01:48:44)
Continuity mistake: When the soldiers bring Indy to Weber, in the background Voller and the two soldiers with the lance can be spotted already leaving. After Weber finishes interrogating Indy, the three Germans are back in their original places with the lance.
Continuity mistake: After Baxter says "It's for you, Doctor", in the next shot, the phone on his left hand disappears. Also, the illumination of the room where Voller goes in changes between shots. (00:47:12)
Continuity mistake: During the conversation in the Tuk-Tuk, Helena's right arm continuously goes from being down to grabbing the roof of the Tuk-Tuk between shots.
Continuity mistake: Voller and his goons are walking through the bridge. Just after Teddy and Hauke fall off, Voller says, "Leave them." Gunther has disappeared. (01:49:22)
Continuity mistake: Weber commands a soldier to open the Lance's box. In the shot of the soldier's hands, a ring has appeared on his left hand. This ring disappears again when Weber says "Doctor."
Continuity mistake: When Helena says "Guten Tag meine freunden", Klaber can be spotted in the background at the cabin already shooting with the machine gun. In a few shots later, he's just arrived at the cabin, holding the weapon, and repeats the action. (02:09:48)
Continuity mistake: Klaber speaks to Voller in German, and then turns and reaches out to grab Indy (all this between the soldiers). But in the next shot, when Klaber grabs Indy, both Americans are now in the cabin. (02:00:02)
Continuity mistake: As the Nazi captain gives orders to the soldiers to grab the sides of the train, the roof of the train is empty. When the captain himself grabs the side of the train, four soldiers appear on the roof. (00:15:40)
Continuity mistake: In the airfield, while Helena and Teddy are hiding behind some barrels, there's a man dressed in brown clothes (clearly not Indy as he's still on the ground) in the background standing behind Voller. This man disappears in the next shot. (01:59:00)
Continuity mistake: Helena places her mug on the upper middle part of a magazine, where a greenish band with the title is. A shot later, the mug has moved to the left edge of the magazine. (02:19:15)
Continuity mistake: When Indy horseback rides on the subway platform, the people stand behind the columns. A shot later from the opposite angle, they're all standing in the middle of the platform.