He kills a bunch of Lex's henchmen in two separate engagements. I didn't have a problem with it personally in that it's generally a part of Affleck's Batman being a guy who's been in the game a long time and has started to lose his sense of perspective -- hence Alfred telling him "everything has changed" and the good-men-turning-cruel speech -- especially after the loss of a bunch of his people in Metropolis during the events of Man of Steel. Comics Batman has killed baddies or left them to die on previous occasions; it depends on who's writing him whether or not he refuses to do this and makes speeches about never using guns or killing being bad.
People have been talking about it since 1989.