Personal viewpoint only, but I would have thought With large formations of aircraft it would be impossible to have all aircraft engines perfectly synchronised. That would have been the unsynchronised beat characteristic of German aircraft over England. Allied bombers operating in similar large formations over Germany would have the same apparent unsynchronised beat as German formations over England. During the period of the war when large numbers of German bombers were flying in formations over England, there were no large formations of British bombers flying over England at the same time.
Thus it would not be possible to listen to both and differentiate between British bombers in formation engine noise and German bombers engine noise. Those that claimed the engine noise was "one of ours" were probably hearing one aircraft - be it a twin engine like a Beaufighter or even a Spitfire. It could also have been one Dornier or one Heinkel.
During the war I saw occasional single German bombers flying at low altitude and do not recall anything unusual about the note of their engines.