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.
Continuity mistake: When they are being interrogated by the gestapo officer, immediately after Anthony Quinn turns the tables on the Germans, Gregory Peck is seen behind him magically holding an MP40 on the seated German officer. The scene then shows Peck picking up the MP40 and threatening the officer again.
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.
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.
Continuity mistake: On the way to destroy the guns the truck hits a tank, and the wheel is bent. A shot later the truck is rolling on with no problems.
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.
Continuity mistake: Gregory Peck, David Niven, and Irene Pappas steal a German army truck while disguised in German uniforms and drive to the Navarone gun barracks to destroy them. Before they get out of the truck the first time the truck is left hand drive. When they get back in the wheel is on the right. Not to mention WWII German military vehicles were left hand drive.