Audio problem: At the beginning of the film, one of the guides goes to shoot Indy with a gun, but as Indy uses the whip to defend himself, the gun bounces off a rock and goes into the water. As the gun hits the rock you hear the sound of the gun firing, but there is no sign of a flash from the barrel or any gun smoke. (00:03:10)
Audio problem: When Marion and Belloq are getting ready to have a drink, as Belloq pours the wine you can hear the sound of the wine hitting ice, making a crackling sound, but there is no ice in the glasses. (01:04:40)
Audio problem: When the camera focuses on Belloq as he looks into the Ark, Toht's screams are inaudible, despite being right next to the Frenchman. Only when the shot changes to show Toht, his screams can be heard.
Audio problem: When the monkey is crawling on Marion's head at Salah's place, the sound does not match Marion's mouth.
Audio problem: In the bar, when the man is shot in the face and burns alive he screams in pain, but he never opens his mouth.
Audio problem: Watch and listen when Marion is being held prisoner in Nepal by one of the thugs. As he seizes her, she's grunting in strain/pain. We can see this in the first, frontal shot of them. However, in the following side shot (from slightly behind Marion as Toht walks over with the heated poker), Marion's mouth is completely still and almost shut, yet her sounds continue (and these sounds would have to be made with wide-spread lips).
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.
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.
Audio problem: After Dietrich pours liquor for himself, he speaks to Belloq. One of the words of his phrase (probably monsieur or Belloq) was cut from the audio as Dietrich's lips still move but nothing can be heard.
Audio problem: Just before Belloq opens the staff car's door, Paul Freeman's voice can be heard saying "Let's get out of here" but Belloq's lips don't move.
Audio problem: After Dietrich says "And Gobler, I want plenty of protection", a German voice can be heard saying "Jawohl, Herr Oberst", just before the tower behind Belloq explodes. This voice sounds extremely close to the three villains, although neither of them have spoken, and there are no more people next to Dietrich.
Audio problem: In Marion's bar, she uses a burning log to knock one of the goons out. As his face changes, you hear "ow!" then he moans as he falls over. However, his mouth doesn't match any of the sounds.
Audio problem: While Indy tries to escape from the Well of Souls a stick in his mouth falls on Marion, who starts to cry very loudly; however, her mouth doesn't move an inch.
Answer: Indy and Marcus Brody believed that the Ark needed to be studied. They certainly didn't want to put it back where it was found. They believed that the U.S. government would find the best archaeologists, researchers, and scientists in the world to study the Ark. They are both upset that instead, the government has decided to simply lock the Ark away. This is why Indy says, "Fools. They don't know what they've got there," as he is leaving the building.
BaconIsMyBFF