Plot hole: Maria describes in lurid detail how Anna was arrested by the Germans and tortured by being severely whipped, leaving her with gruesome scars all over her back. She also says that Anna hasn't spoken a word to anyone since she escaped from captivity. How, then, does Maria (or anyone else) know about the scars? Nobody saw them (they don't exist) and Anna obviously didn't tell anyone about them.
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.
Plot hole: The huge guns are set high up on a cliff face facing out to sea and it is obvious that they cannot be depressed to fire at a downward angle - the massive gun carriages set on rails would prevent that happening. They cannot be elevated to fire at an upward angle, too, because they fit pretty snugly in the hole cut into the cliff face to accommodate them. This means that their maximum and minimum ranges would be quite close together, covering a strip of maybe a few hundred metres either side. Given that the sea is completely open on the side of the island they are protecting, why don't the ships targeted by the guns while passing the island simply sail inside or outside of the narrow stretch of sea the guns can hit?
Other mistake: At the beginning of the film a bomber is crashing. As this is happening another bomber is stationary in the sky.
Continuity 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 the girl is killed by Maria we see a shot of her from the shoulders up. She is not shot in the head so we can only suppose that has been shot in the heart (for her to die so quickly) but when Brown checks her out there is no blood and no exit wound on her back. So where was she shot?
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.
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.
Audio problem: When Maria is talking to the other woman at the ruins after she comes to, the last time she says, "Our friends," her lips don't match the words.
Other mistake: Throughout this movie it is stated that Mallory can speak German "perfectly", that is, without accentual or grammatical problems at all. But Gregory Peck's 'German' throughout the movie is obviously less than perfect. (I ought to know; I live in Germany and speak both English and German well enough to notice the difference.)