What's ironic about Peter's apology to Ender in Chapter 2 of Ender's Game?

Peter's apology to Ender after tormenting him  (Peter had been rejected by the government, in large part because of this cruel streak in him), and in his jealousy makes Ender and his sister Valentine wonder when he will strike again ( Peter is a master manipulator).  So Peter's late-night apology could be a sudden and brief regret, an actual "change of heart," or part of his calculated plan.  Card, early in the novel, is purposely being vague about Peter's motives.  The main plot of the book--Ender's training and "game"--is bracketed by the plot of the family dynamics, which includes Ender's close relation with Valentine.  The larger theme--can war be averted by trying to understand alien cultures--puts this Bildungsroman in the high category with Catcher in the Rye and Lord of the Flies.

What's surprising and ironic about Peter's apology to Ender?

It looks like you are referring to the novel by Orson Scott Card, Ender's Game.

In Chapter 2 (eNotes has chapter summaries for this novel), we are shown that Peter is actually a very sadistic and manipulative older brother. He is envious of Ender and complains that Ender was monitored until he was six while Peter was only monitored until he was five. Although Ender is a legal Third child (the government only allows two children per family), Peter taunts Ender about the legitimacy of his existence. Yet we get the idea that there is something special about Ender. Perhaps this is why Peter is jealous of Ender.

In this chapter, Peter forces Ender to play Bugger And Astronauts with him. "Bugger" refers to the alien race that is the great enemy of Earth. The game provides cover for Peter's violent attack against Ender. He threatens Ender and claims that he will eventually kill him. Their sister, Valentine, intervenes, only to be threatened by Peter as well. However, she claims that she has already planned for such a contingency. She tells Peter that she has kept a secret letter hidden at the public library delineating Peter's guilt if he ever kills both her and Ender.

Later that night, Peter apologizes to Ender; his apology is ironic due to his earlier and typical acts of violence against Ender. We are left to wonder if he is only being manipulative and/or just biding his time until he can find some way to circumvent Valentine's seemingly air-tight maneuver regarding the secret letter.