I think that one specific difference between the book and the film is the ending. The ending to the film is the closing of the gas chamber door, the camera panning from it. The reader is left with this as the closing image. In the book, there is a follow up in terms of what happened to Bruno's family. The other primary difference in this regard is that the ending of the book is one in which Boyne is able to insert the closing thought of whether something like the Holocaust could happen again. The ending to the book seems to trigger more in way of reflection and thought in the reader, as opposed to the film where it is more of a visceral and emotional reaction to the deaths of Bruno, Schmuel, and millions more.
In a small, but significant difference, Bruno's mispronunciation is not seen in the film. The lack of "Out- With" and "the Fury" in the film takes a bit away from the emotional and thematic significance of Bruno not being able to correctly say things that exist beyond the pale of language to describe. At the same time, this helps to make Bruno in the film appear to be a bit more knowledgeable about the world than he is shown to be in the book. It also helps to construct a film version of Bruno that slightly lacks the childlike wonder that is present in the book's characterization.