Factual error: Miller rigs his booby trap by attaching the wires from the bomb to a pole down which a metal runner slides, so that when the runner touches the wires it completes the circuit and detonates the bomb. The trouble is, the pole is made of steel, and steel is very conductive indeed. Miller attaches the exposed end of the wire to the pole without any insulation or gap. The circuit will actually be completed when Miller attaches the battery, and he and his booby trap will be blown sky high.
Factual error: When the commandos are heading to Navarone by fishing boat, they are buzzed by the piston-engine high-wing observer plane (looks a lot like a tricycle-gear Cessna, not around in that period). As the aircraft passes it sounds like they were buzzed by a big powerful craft, like a Mustang or a Spit.
Factual error: During the train ride scene, the train is being pulled by a modern Yugoslav railways electric locomotive, despite that it was manufactured postwar and that there were no electrified rail lines in 1940s Yugoslavia.
Factual error: Captain Sessler, the SS officer who questions the commando team, has no SS sleeve eagle on his tunic. Also, the eagle on his cap is the Heer (regular army) style rather than the regulation SS style.
Factual error: In the German office, after overpowering their captors, Mallory gives a pack of cigarettes to the wounded Major. The pack contains filtered cigarettes, which were not readily available. The only commercially made cigarettes at that time were available in Yugoslavia. England had filtered cigarettes with an attached tip that were special order. The Yugoslavian filters were made of crepe paper and not the cellulose ones on the cigarettes in the movie.