The word prejudice naturally holds a negative connotation and most often brings to mind racial or gender bias first. Ironically, though there are racial and gender differences presented between characters, the idea of prejudice is not presented negatively from character to character.
At battle school, it is common knowledge that students in attendance are the best and brightest from around the globe. Naturally this makes them all racially different from one another. Rather than looking at each other with prejudice however, the racial differences are simply set up to characterize differences of attitude and opinion. For example, Bonzo is known for his Spanish pride. Rose the Nose is Jewish, and while the racial slur "Kike" is mentioned, it is not done in an offensive way. Rather, it is almost in jealous praise of the political success of Jews in the context of the story. In the first version of the book there is a scene involving Ender and Alai, joking about slavery. In this scene (which was later removed by the author) the n-word is used. Again, it is done very casually and not at all offensively, almost to point out that the prejudices that may be present in the minds of the audience have faded out in this future version of Earth. Finally, Petra is pointed out as the leading female in the Battle School, and though she is not a boy, she progresses quickly and experiences much success. Her struggles of being a girl are not necessarily outlined, except in the one instance of Bonzo treating her differently from the rest of his army.
On the other hand, the one prejudice that is emphasized in a negative way, is the attitude humans hold for the Buggers. Even the very term "Bugger" is a word of contempt or a slander against someone. In fact, Bugger is not a technical term at all. The aliens are referred to as such because they so closely resemble ants or bees: bugs.
In this way, the lack of prejudice between humans heightens the unified prejudice against the Buggers. It is natural, when you think about it, to attempt to get the entire population to hate the beings which attacked Earth. Because there was no communication with the Buggers, the government had to assume they were only a threat, and seek to destroy them. This doesn't, however, subside the guilt that we, as humans, were killing another living being. By emphasizing the Buggers lack of humanity and their enmity toward humans, it was easier to justify destroying them as a race.