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It appears there was something like a transient mutiny, or 'something' on U530
Investigators from the Argentine Navy came to the conclusion that there had been a mutiny on U 530, according to which Commander Wermuth did not command the boat continuously. Since the logbook or war diary was untraceable, the exact details of the voyage remained in the dark. Otto Wermuth was described as small and dark-haired. It was therefore suspected that the tall blonde Otto Wermuth, who had brought the boat to Mar del Plata harbour, had been a swindler who had boarded only shortly before, and had possibly only boarded shortly before on the Argentine coast. To support this view, it was argued that he had been very vague about the exact details of the voyage. In addition, Wermuth testified that the deck gun had been taken off the ship in Germany and left behind at the quay, while the crew unanimously stated that they had dismantled it and sunk it overboard into the Atlantic.
Src: German Wikipedia: U 530
Given the cloudy knowledge of that particular incident, there seem to be no historically approved mutinies of that kind depicted – on a u-boat.
But that doesn't mean there were no mutinies at all. There were 22000 death sentences during the war. It seems that the most famous mutiny was aboard a Minesweeper: M 612.
It looks like that is exactly that what was depicted in the series?