Revealing mistake: When the water floods the mine, some shots of the 3 heroes are an obvious composite of their blue screened image over a set. Problem is, when Indy tells the two to run towards a tunnel on the right with a log blocking the way, Indy and Shorty run through the log as if they were ghosts.
Revealing mistake: When Indy is hanging on the cliff as it falls out from underneath him (right after the mine cart scene), as he's kicking, you can see the stone wall moving in and out as he hits it after the rocks fall out underneath him.
Revealing mistake: When Willie runs into the death pit after pulling the release lever, when she drops the lantern Indy is not Harrison Ford but a stunt double. (00:59:30)
Revealing mistake: At the bar Indy has swords thrown at him. The string to make them fly is visible attached to the sword on the left side. Also, the swords disappear in the next angle.
Revealing mistake: After Indy drinks the antidote, many of the chase-scenes are obviously sped up, watch the way the actors move.
Revealing mistake: When Indy is put inside a cage Short Round comes to hug him. There's a shot of Indy from behind and he is a noticeable stand-in: Thinner face, clean hair, no sweat, and clean shaven instead of stubble.
Revealing mistake: When Indy is whipped six times, the first time we can see the whip doesn't touch him, or go anywhere near him.
Revealing mistake: When Indy wraps his whip around an assassin's neck and hangs him on the fan, we can see it's not actually around his neck, it's just attached to his clothing.
Revealing mistake: When the 3 heroes exit the mine cart and escape from the water flood in the mine, Harrison Ford is replaced by an obvious stuntman.
Revealing mistake: When the water tank falls over, the vapour fumes are moving in slo-mo, despite the whole scene moving at a normal speed.
Revealing mistake: When Willie and Short escape the jet of water and Indy climbs the mountain alone, the river below is totally still (impossible because of the huge amount of water that's falling on it), revealing it's a still image.
Chosen answer: His neck was snapped by the whip getting caught in the fan. There isn't always blood with a hanging. Since the fan wasn't designed to hold a man's weight, the motor in it would have stopped or given out.
Captain Defenestrator