Asking how Gene was alienated in A Separate Peace is a bit of a tricky question because Gene is our narrator and we only get the events from his perspective. Not only are we getting it from Gene, but a much older Gene who has had years to solidify in his own remembered history the events that have occurred. Gene, even into his adulthood, carries a strong sense of guilt, and it may be that the guilt he feels distorts how things were. Where his friends may have seen him as part of the group, Gene himself may remember being alienated.
Though Gene is not a trustworthy narrator, it could be argued that much of Gene’s alienation stems from his comparison to those around him. If his friends seem to be looking up to others then they are not looking at him, which might lead to his feeling of being outside the group. Remember, Gene goes to school later than the other boys do. At this point, patterns and friendships have already been established, leaving Gene to figure out his place. He is assigned to Finny, and this starts their friendship and sets up Gene’s place in the group as Finny’s roommate, though Finny regards Gene as his best friend. In Gene’s mind he is only there because of Finny and does not see himself as part of the group. When Gene attempts to establish his belonging through his academics, Finny, according to Gene, is attempting to keep him from succeeding, thus keeping Gene connected to the group as only the roommate/friend of Finny and not a real part.
We know that Gene’s memory of events is suspect, as seen in the trial when Lepellier expresses what really happened at the tree. We know that the narrator is a much older Gene relaying the events of his youth. We also know that these ideas do not devalue what Gene felt or how he remembers them and this ultimately makes his feelings of alienation true for him and the reader.