"Who are all those people? […] And what are they all doing there?" (4.190)
Bruno asks this question out loud to himself when he sees the prisoners for the first time on the other side of the fence. At this point in the novel, he does not know that the majority of them are Jews (nor does he realize that he is no longer in Germany).
[…] [The prisoners] were wearing the same clothes as each other: a pair of grey striped pajamas with a grey striped cap on their heads. (4.204)
Bruno is confused as to why all the people wear the same uniform. The only sense he can make of the clothes is that they're all in pajamas. What could be so bad about spending all day in your pajamas, right? Oh so much, Bruno—oh so much.
"Ah, those people […]. Those people… well, they're not people at all, Bruno." (5.283)
Bruno's father, like many of the SS, believes Jewish people are an inferior race, and therefore, not really people. Of course, he doesn't ever bother to explain to Bruno the exact details of why race is involved—or that they're killing the Jews.
"They're nothing to do with you. You have nothing whatsoever in common with them." (5.284)
Again, a common misconception: Jews and ethnic Germans have nothing in common. Of course, Bruno's father is more wrong than he could ever imagine because his own son is actually best friends with a Jewish kid. Oops.
"Heil, Hitler." (5.288)
When Bruno says this to his father, he admits to himself (and readers) that he thinks it's another way to say goodbye or "have a pleasant afternoon." We're not too convinced about that, though, since he speaks German and should know exactly what it means.
"Well, you've been brought here against your will, just like I have. If you ask me, we're all in the same boat. And it's leaking." (6.305)
A pretty profound thought from Bruno, no? When he tells Maria this, we can't help seeing the relation to the situation at hand: Jews were forcefully taken from their homes and brought to Auschwitz as prisoners—and sooner or later, the Nazi boat is going to sink.
[…] [Bruno] looked across at Maria and realized for the first time that he had never fully considered her to be a person with a life and a history all her own. (6.319)
Talk about deep. Bruno has his very own eureka moment when he sees Maria not as the maid, but as a person with feelings, emotions, and a family. We think this is why he can so easily talk to her, Pavel, and Shmuel—because he sees them as people and not for their labels.
"Come over here, you—" (7. 390)
Lieutenant Kotler orders Pavel to help Bruno make a tire swing, and calls him an ugly name several times. Boyne chooses not to print the name, but it's probably safe to assume given the context (and Kotler's character) that it's a derogatory term for a Jewish person.
"About the great wrongs that have been done to you." (9.508)
Like Bruno, we're left pretty perplexed by Herr Liszt's insistence that "great wrongs" have been done to Bruno and Germany. We're never told about these wrongs, and Bruno never brings them up either. Talk about vague.
On [Shmuel's] arm he wore an armband with a star on it. (9.535)
This is the first time Bruno sees the Star of David, which Shmuel and the other prisoners wear. He doesn't ask what it means, but we know that it was a way for the Nazis to further discriminate and distinguish the Jews from the rest of the population.