I have 2 books about submarines that report at least 3 or 4 cases where this happened. It happened on the japanese, american and german side. One of the books is from Franz Kurowski who was aboard a german U-Boat himself and he tells one such case where a german commander did this (who was later court-martialed after the war and shot). The other book reports a rather famous american commander killing japanese survivors (and one japanese survivor trying to throw a handgrenade at the sub in another case) and the japanese seem to have shot at survivors more than once according to the book.
Link :
http://en.wikipedia.org/wiki/Dudley_W._Morton
War destroys not only the victims.
