I do believe that one US sub was either lost or seriously damaged due to fratricide during WWII.Of course a few times US subs and aircraft also sank ships loaded with POWs but they could not have known because the Japanese did not mark transports when they where carrying POWs.The same could apply in an open war zone you could expect any naval vessel friend or foe to be dangerous(when the friend does not your present) they did have light coded challenges to try and avoid this also a US sub could "ping" a buddy but how can the buddy know that the japs did not deploy sonar and he is discovering it?
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