Minor plot hole: The staff that reveals the location of the map is said to be 6 kadams, or 72 inches tall, minus 1 kadam, or 12 inches. For those of you who skipped elementary school entirely, that's 60 inches, or 5 feet. Yet the staff towers at least a foot above Indy, meaning that either Indiana Jones takes place in a universe of midgets or Steven Spielberg underestimated the will of nerds to decipher everything in his movies. There is also no real reason to write instructions on the medallion this way. When was the last time you looked at the instructions on a frozen pizza that said 'cook me for 20 minutes minus 5’.
Minor plot hole: Indy and Marion are thrown into the well of souls, the place where the ark of the covenant has been buried for hundreds of years. However this chamber has natural light in abundance, and plenty of snakes, who for whatever reason, like to hang out in great numbers in underground chambers with no food.
Minor plot hole: Once Indy is done using the staff to determine the location of the well of souls, he snaps the staff in two so the Nazis cannot use it. This however, is stupid beyond words. The staff itself is of no importance, it is only the length that matters. And I doubt it is beyond the wit of Germany’s finest minds to determine the length of a staff when they have both of the pieces. Just because you had trouble with working out the length Mr Spielberg, doesn't mean that the rest of us are morons.
Minor plot hole: There are hundreds of Nazis, archaeologists, and assorted Egyptians all over this desert area, searching for the Well of Souls. They are digging, looking on maps, searching everywhere. Of course Indiana Jones finds the place, discovers the ark, Marion is tossed in the hole etc. They need to escape from this place.
Finally, they manage to smash through a wall, and Indy looks up and sees a ray of sunlight. "A way out!" he says. They climb up...At this point, they push this big brick out of an ancient wall. Indy looks out of the hole left by the brick, and they are sort of behind some German army tents. In the distance, you can see the airplane loading up the ark. Now the question is... this wall is clearly observable from the outside. Why did nobody ever ask, "hey, what is that ancient looking wall over there? Maybe we should check that out." Because if they had, of course it leads right into the well of souls etc. etc. No digging around in the sand... like the external wall of the place is clearly observable right next to the Nazi's tents.
Major plot hole: Indy finds that the Nazis are digging for the ark in the wrong place, but not by much. Indy, Marion and some others dig for the ark in the correct place, which is walking distance from where the Nazis are digging. Of course, none of the hundreds of Nazis on the digging site notice Indy’s separate digging party.
Major plot hole: No list detailing Indiana Jones plot holes would be complete without the infamous submarine scene. Our hero swims to a German u-boat that is about to dive, where he grabs on to the periscope and should drown. Or maybe get hypothermia, or be discovered by the patrols that would be on deck whenever the sub was above water. What should not happen is that he would be able to sneak aboard the sub or cling on to the periscope and hold his breath for the entire journey. Exactly how he does this is unknown, as the next scene shows him inside the sub, a tad wet, but otherwise alive.
Plot contrivance: Indy thinks Marion is dead, as he saw the truck he believed she was in explode. However she turns out to be alive and well, as when Indy is escaping the Nazis digging site, he just so happens to stumble into a tent in which Marion is tied up. This was one of hundreds of tents, and he fell in the good one on the first try.
Plot contrivance: Toht is able to produce an exact replica of the medallion for the Nazis because he had an imprint of it burned on his hand from when he grabbed it in the burning bar. However the idea that a few seconds holding a hot object would give you a perfect copy of all the writings on the medallion, let alone the precise cuttings of the crystal is ludicrous.
Plot contrivance: How did the ten commandments erode into sand? Usually that takes air and water to achieve.
Unadressed Issue: When Indy and Marion are tied to the post and Belloq opens the ark, Indy tells Marion not to look at it and apparently this is why God spares them. How does Indy know this? It would have been nice if this had been set up, if for instance someone had said "Anyone who looks on the ten commandments will be killed in horrible ways". But in it's current form Indy just looks like a sociopath.