Factual error: During the travel to Nepal, "Thailand" is written on the map. The country has had this name only since 1939. This film takes place in 1936, when Thailand was called Siam. (00:23:20)
Factual error: The interior of the German U-boat is completely different from the real interior of a Type VII U-boat, which is correctly shown in movies like 'Das Boot' or 'U-571'. For example, the ladder from the conning tower faces a different direction, the map table is too big and on the wrong side, the valves for submerging are on the side of the control room and not at its front and stern, depth gauges are too big...etc. All interiors were standardized, so it could not have been an individual build.
Continuity mistake: Just before the car carrying Marion in the wicker basket explodes in the alley, Indiana shoots a man twice in the chest. The man has blood stains on his shirt before he is shot.
Continuity mistake: As Indy and Marion are starting to run from the plane, you can see the yellow wheel chocks are back in place under the plane's tires.
Continuity mistake: After hitting one thug, Indy jumps out of the way of one trying to spear him, leading to the one behind Indy getting run through. As the guy gets run through, he is in front of a hanging string of fruit, with the stacked fruit to his right. After a cut scene to Indy and Marion running away, the run through thug is now facing the fruit stand, setting up the sight gag of the blade sticking out with two fruits stuck on it.
Continuity mistake: At the beginning of the film, When Indy uses the whip to take the guides gun away, Satipo makes a weird face and starts to move away in amazement. The very next frame, in a wider shot, he is not finishing his movements, but on the contrary he is standing still, with a normal gesture, until a second later he starts to repeat the movement and looks from before.
Continuity mistake: When Indiana is hiding his face with the cloth, watch as he enters the tent that Marion is being held prisoner in - at first, Indiana has to hold it in place; in the next shot, he has it tucked into the rest of the folds. The next shot, the actual position of the cloth changes.
Factual error: At the beginning of the movie, Indy escapes in biplane with registration OB-CPO (a Star Wars nod, as noted in trivia). However the OB registration is used by Peru, and it should be followed by four digits, not by three letters. (00:12:10)
Suggested correction: Simply not true, as with most countries with two-letter civil aircraft registrations, Peru used the XX-YYY format at this time: http://www.airhistory.org.uk/gy/reg_OA-.html.
Revealing mistake: The Pan American aeroplane Indiana Jones boards in San Fransisco looks similar to (but has noticeable differences from) the Boeing 314 PanAm used for transpacific flights. This aeroplane did however not fly until 1938 and at the time of the story the company only flew transpacific with Sikorsky S-42s, an aeroplane with a completely different body than the one used in the scene.
Revealing mistake: When Indy is fighting the big German at the base of the airplane, Indy reaches down and grabs a handful of sand to throw in his face. You can see the finger marks in the sand from a previous take.
Audio problem: When Marion meets up with Indy on the steps of the building at the very end of the film, she asks what was going on in there. Her first few lines of dialogue were dubbed in after shooting. Her mouth isn't moving with the dialogue.
Continuity mistake: When Indiana is fighting the Big German mechanic by the plane, the plane goes around in circles and the wing tip of the plane punctures a hole in a petrol tanker that is parked near by. This causes the petrol to gush out of the tanker and you can see that ground underneath the plane gets totally drenched with petrol. But in the later shots, the ground under the plane is dry. There is also a shot where you can see the tanker in the background not pouring petrol any more and all you can see is a little wet spot around the tanker. (01:18:45)
Revealing mistake: When we have the exterior shot of the ship that Harrison Ford, Karen Allen, and the Ark are aboard, specks of dirt can be seen over the view of the ship and the ocean - obviously, it was filmed through the window of another ship. (01:31:35)
Factual error: Several times during the movie, Indy is under fire from Nazis or other bad guys wielding what look like MP-38 sub machine guns. The movie is set in 1936, 2 years before the weapon was even designed. The Erma EMP-36 has wooden parts (the grip), the muzzle spike at under the barrel is more pointy and the front sight are more massive than MP-38/40, and the magazine is tilting slightly forwards towards the muzzle. The MP-38/40 is all stamped sheet metal (no wood, because it would slow down production), the muzzle spike under the barrel is more smooth (maybe so it won't get stuck?) and the front sight is more simple (basically just a ring with rumble strips) than the ERMA's, and the magazine on the MP-38/40 is vertical.
Continuity mistake: When Belloq talks to Indy in the Well of Souls the two Arabs on the left disappear in the angles from Indy's POV.
Continuity mistake: After Satipo runs with the idol, Indy grabs a root to help him climb up the ledge. Half a second later, from a different angle, the root is meters away and he is grabbing it again, repeating the whole scene.
Continuity mistake: After Indy rips a big strip of Marion's dress in the Well of Souls, it continues to change until she finally gets rid of it on the boat. At some points (eg. running from the plane before it explodes, and other shots) it seems quite straight across, more like a shorter dress than a torn one. A few moments later, when they are crouching behind an earth bank and Sallah tells Indy the Germans are putting the Ark on to a truck, the dress is badly ripped in various places across her back. Not long afterwards, it is in one piece again but back to the bottom edge being ripped. (01:13:00 - 01:21:35)
Continuity mistake: When Indy climbs onto the pontoon of the airplane from the lagoon in the opening sequence, he is obviously wet from swimming in the lagoon. However, in the next scene as he climbs further, his clothes are miraculously dry as observed by watching them blowing freely during take-off. (00:12:05)
Audio problem: When Toht walks in with Dietrich and Gobler, watch the background, you will see Dietrich's lips moving, but you cannot hear him saying anything.
Continuity mistake: Indy looks at the Wurffler through the binoculars. In the next shot, when he takes them off and looks at Katanga, the submarine has moved to the left and astern. (01:34:58)
