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 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 Mongolian is shot at 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: 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: The scene you describe was indeed filmed. It was cut out of the US release of the film although I cannot speak for the Australian version. The scene also appears in the Marvel Comics adaptation. http://www.theraider.net/films/raiders/deleted_scenes.php has a list of this and the other deleted scenes.
Phil C.