"Plot Holes" and how to deal
My angry, embittered, and occasionally constipated brother-in-arms has done a good piece of research and logic rebutting a couple Raiders Of The Lost Ark "plot holes". They really aren't plot holes, per se, but somewhat unrealistic events that the viewer found disagreeable. The gripe (from here):

Perhaps the greatest came in Raiders of the Lost Ark. Nazis steal the ark from Indiana Jones, and escape in a U-boat. As the submarine dives, Jones leaps off a ship and clings to the U-boat's side. Now, what is he supposed to do -- hang on while the sub is underwater? We see a chart of the U-boat crossing the Mediterranean, then a shot of the submarine easing into its dock at a super-secret base. As the submarine arrives, Indiana Jones is already standing on the dock, disguised as a Nazi. Double plot hole! Not only could he not have survived by clinging to a diving submarine, how did he then get to the base first? Triple plot hole! How did he even know where the sub was going?

Jaquandor does address both amply. But I think there may be more to it (thusly indulging my ability to over-analyze everything). As you may (or may not) recall, Indy is not already in a Nazi uniform when he first appears behind some crates. He is forced to knock out a Nazi soldier and take his uniform -- only the uniform doesn't fit so he takes the one of the officer who accosts him for being unkempt, adding a bit of comic relief to the moment. This scene also serves as a nod from Lucas/Spielberg to the cliche of interchangable, one-size-fits-all garments that always seem to be worn by the abductees.

However, in light of the "plot hole" described above, the placement of this little scene serves a third purpose. It is a wink to the audience that every movie has little "plot holes" or unrealistic situations (not the least of which is that 'Lost Ark' is a fantasy movie for pete's sake), such as the Indy's journey on the submarine the scene before. This isn't lost on the movie-makers, so instead of ignoring what has transpired, they chose to include a short, comic scene that says "Yeah, we know it's a little unrealistic, but this is just a movie".

My work here is finished. You are all enlightened; admit it. Or scared.