First of all, the movie is set in the late thirties, well before WW2 broke out, so there would not be any problem with German submarines going whereever they wanted. Second of all, submarines in those days did not travel underwater. They were not yet nuclear-powered, and so it cost more power and they could not move as fast while they were submerged (for example, a Type VII U-boat [wihch was staet of the art in 1936] could only make about 7-8 knots while submerged, compared to over 17 knots on the surface), AND they could not stay down for nearly as long. Submarines submerged like soldiers crawled on their bellies - when there was enemy activity nearby. No way a submarine COULD or even WOULD travel submerged the distances shown on the map in 1936/37. They only dove to avoid being spotted when they KNEW something hostile was nearby.

If they wanted to nit-pick about military hardware, there is the dubious issue of sending a sub to pursue a surface vessel, as many ships could outrun even the best submarines in the 30s(though they might have simply radioed ahead to have a sub in the area intercept it). Or they could bring up the rocket launcher Indy points at the Ark. The first rocket launchers like that were invented by the US and only deployed after we joined the war in 1941, and the Germans only built their version (the panzershrek) after capturing American models to reverse-engineer is Russia, which, again, they did not invade until 1941. So there would not have been a bazooka or panzershrek for Indy to threaten the Ark with in 1936 or whenever the movie was set. Also, I suspect the gun that Indy used to shoot the guards who entered his father's room (before saying "Don't call me Junior" ) in the third film was a MP-40, which, as the name implies, was not available in the 30s. There were German predecessors to that weapon, though I am not confident of a visual identification.

By this standard, planes can't REALLY fly either, since they cut to the map for that too.