Visible crew/equipment: During the jungle chase, Marion jumps out of the truck, leaving Dovchenko driverless. A few shots later, Spalko fires on the two amphibious vehicles, and when Mac removes his cap to check his head, the actor's modern wired device (earbud or mic perhaps) drops out from under his scarf/shirt and hangs over his shirt. Later, in the chamber with the crystal skeletons, Mac admits to lying about the CIA, then as Spalko climbs the chamber stairs, it looks like her lav mic is a bit visible between two upper buttons. (01:17:10 - 01:44:15)
Continuity mistake: Before being knocked by Mac, a Russian soldier throws the Skull to Spalko, who has her rapier in her right hand. In the next shot, the rapier is in its sheath. (01:18:48)
Continuity mistake: After Mac knocks the Russian soldier out of the car, the position of Oxley's head and arms changes in the next shot. (01:18:49)
Continuity mistake: When Spalko is trying to throw Indy's car off the cliff, the knocked-out soldier in the passenger seat of the amphibious car is suddenly conscious and sitting between shots. (01:22:30)
Continuity mistake: During the siafu ant attack, while fisticuffs ensue between Indiana and Dovchenko, note the direction of Dovchenko's belt, with its buckle prongs to his left. Then, when Dovchenko falls backwards and the ants swarm all over him, his belt is worn around his waist the opposite way, with its prongs to his right (neither are flipped shots). (01:26:55)
Continuity mistake: Inside the waterfall temple, the group walks by a room (with a passage on each side and a double entrance with steps in the middle) where natives appear and columns and walls fall off. The angle changes to a seemingly new room, but it's obviously the same place, with the camera angle slightly turned to the right. All the previous people are magically gone, the debris has disappeared, and natives are coming out of different places. Really odd editing. (01:30:35)
Visible crew/equipment: After everyone has fallen into the water beneath the obelisk and the skull has been retrieved, Indiana is leading everyone out of the water and a prop light can be seen on the big rock spike behind Mutt. (01:40:25)
Factual error: In the wedding scene, the minister uses the modern, politically correct "I now pronounce you husband and wife" instead of the traditional "man and wife" - unheard of in 1957. (01:54:50)
Continuity mistake: At the beginning when Indy is talking to Spalko, his hands keep alternating from being in his pockets to just resting at his sides between shots.
Factual error: In the warehouse scene, the lights and other metal objects are affected by the box's magnetic field. Yet the soldiers easily lift the box into a metal truck to load it and slide it forward. If the box's magnetic field was as strong as suggested, it would have dragged the soldiers forward as it was magnetically attracted to the truck, and it would have taken much more effort for them to slide it onto the truck bed once it was stuck there.
Visible crew/equipment: When Dr. Irina Spalko is descending the cliff, you can briefly see the harness cable that is holding her up right next to the rope on which she is climbing down.
Factual error: The 1950s kitchen scene shows a sink faucet "Dishmaster Model 87" which wasn't manufactured until 1987. The 1950's "Dishmasters" were different.
Factual error: The movie supposedly is set in 1957, yet Mutt's motorcycle is based on a 2000 or newer Harley Davidson softail, showing the modern-day controls and Twin Cam motor, instead of the panhead motor that would have been the period-correct engine for 1957. It also has a front disc brake - you can see the master cylinder on the handlebars. Again, out-of-place on a 1957 bike.
Continuity mistake: After Indiana and team fall off the disappearing stairs as they make their way into the lost city, they are walking around in the water. But when they step through the next door into the treasure room, all are completely dry.
Factual error: Indy and Mutt fly to Nazca, Peru. Nazca is only 4 hours away on bus from the capital Lima, yet the city they show on the movie is Cuzco, which is 24 hours away from Lima. Cuzco is on the east side of the country, Nazca is on the west coast right next to Lima. Also, back in 1957 only Lima had an airport, yet they show a Nazca airport that didn't exist.
Plot hole: Hiding in a fridge (or anything else) in order to be conveniently blown out of the way by an exploding nuclear device is absurd beyond belief. The fridge is just so much extra reaction mass and would be vaporised by the expanding nuclear explosion - it wouldn't be daintily picked up and thrown a few kilometers to safety. If it was, why doesn't it land in a shower of similar artifacts which have also been dislodged and thrown around? Incidentally, even if it was thrown out of the way as shown, anyone inside it would be turned into a smear of strawberry jam by the acceleration required to beat the shock and heat wave of a nuclear blast, and then liquefied by the deceleration involved in hitting the ground at that speed.
Continuity mistake: When Indiana and Mutt are in the diner, at the start of the scene there is a pretty blonde girl sitting at the counter just past the corner. A moment later, her seat and the one next to it are occupied by the two Russian guys in suits, and she is talking to a guy with glasses who was earlier by himself. Not enough time had passed for that to change.
Factual error: When Indy and Mutt are flying to Peru, a Pan American Aircraft is shown. It is an Antonov AN-2. Pan Am never flew this Russian aircraft! Also, the shot is backwards; the writing on the aircraft (airline name and registration) read backwards.
Factual error: During the motorcycle chase seen (which was filmed in New Haven, CT) one can see modern yellow traffic lights covered in burlap in a few of the scenes.
Factual error: The movie shows Mayan warriors talking Quechua in the Peruvian jungle instead of showing Inca Warriors.