What is surprising and ironic about Peter apologizing to Ender in Chapter 2?
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.