Could it be said that "The Boy in Striped Pyjamas" contains a form of irony in the way that Father thought he was killing the enemy; not his son?
Indeed, the ending to "The Boy in the Striped Pajamas" is ironic. It's painfully ironic. If we operate on H. W. Fowler's definition of "irony" such as, "that the surface meaning and the underlying meaning of what is said are not the same," we can apply Fowler's understanding to Boyne's novel. The fact that Bruno's father operates as an extension of the Nazis, promoting its values and living his life in full confidence of what is being done in the Holocaust, would represent a surface meaning of the narrative. Running contrary to this surface meaning is Bruno's befriending of Shmuel. The fact that the father's orders to round up the prisoners for mass execution would involve his own son, wearing "pajamas," is ironic because the surface meaning of the father's actions contrasts with the underlying meaning and the implications of them. He is left to fully understand this at the end of the novel. The historical irony that is also present is that the Holocaust ended up killing both the victims and the agressors' sense of humanity. When the father recognizes this, he might actually be mourning for both his son and his son's dignity.