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.