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.
Continuity mistake: When the Germans are cutting through the bunker door at the mountain complex, the interior shot shows them having cut a hole of at least 2 feet in diameter, but when the guard on the outside shoots through the hole in the door, it is only about 12 inches by 4 inches, no way they could have cut the interior door through that small slit.
Other mistake: At the beginning of the film a bomber is crashing. As this is happening another bomber is stationary in the sky.
Other mistake: Towards the end, when the Germans are searching for explosives around the guns, there are several Germans using metal detectors, yet they are walking along the steel rail tracks and around metal shells and ammo boxes.
Other mistake: When the fishing boat is stuck at the base of the cliff we see it tossing and rolling. However, when Brown is in the hold there is no movement. Also when the men are unloading their supplies the boat is obviously fixed and stationary.
Continuity mistake: When David Niven is at the bottom of the hoist setting the explosive charge, his hands are covered in grease as he is hiding the wires, which would complete an electrical circuit. Seconds later, when he and Gregory Peck are moving toward the guns his hands are perfectly clean. There was no time to wash his hands - or any evidence of a sink - when the Germans were feverishly trying to get into the tunnel.