The famous scene in which Indy shoots a marauding and flamboyant swordsman was not in the original script. Harrison Ford was supposed to use his whip to get the sword out of his attacker's hands, but the food poisoning he and the rest of the crew had gotten made him too sick to perform the stunt. After several unsuccessful tries, Ford suggested "shooting the sucker." Steven Spielberg immediately took him up on the idea, and the scene was successfully filmed.
Steven Spielberg has said that he considers it the most perfect film of the series. He never wanted to modify it or change anything about it.
When Brody first goes to Indy's house to discuss the mission, Jones is dressed the way he is because he is entertaining a young woman in his bedroom. The script originally planned to show her before moving to the next scene, to give Indy a more worldly persona (like James Bond). However, her appearance was cut, as Steven Spielberg thought that being a playboy did not fit Indy's character. (This also helps explain why several of the co-eds fawn over Jones and why one girl wrote "love you" on her eyelids).
While filming the snakes scenes inside the Well of Souls, a python bit first assistant director David Tomblin's hand and wouldn't let go. Tomblin calmly asked someone to grab the python (still attached to Tomblin's hand) by the tail and whip it, so that the snap would send a wave up the snake's body and force it to let go. A stage hand did just that, the python released its bite from Tomblin's hand, and Tomblin got medical attention. The python itself was not injured.
During filming in Tunisia, nearly everyone in the cast and crew got sick except director Steven Spielberg. It is thought that he avoided illness by eating only the food he'd brought with him: a lot of cans of Spaghetti-O's.
Frank Marshall: Pilot of the flying wing. All the stuntmen were sick on the day that Marion hits the pilot of the Flying Wing over the head, so producer Frank Marshall agreed to do it. Unfortunately for him, the shot took three days, and a lot of it involved him sitting in a cockpit that was in excess of one hundred degrees.
Terry Leonard: The stuntman who appears as the German truck driver also performed numerous stunts as Indiana, including jumping from the horse to the truck and sliding under the truck.
Dennis Muren: Appears as a Nazi spy who is tracking Indiana Jones on the airplane. Only his eyes can be seen, though, as most of his face is hidden behind the magazine he's reading, which is Life volume 1 number 2 (November 30, 1936), which has pages 42-43 dedicated to the water color paintings of Adolf Hitler.
Glenn Randall Jr.: The stunt coordinator appears as the mechanic with the monkey wrench at the flying wing.