All the enmity in the novel comes from Gene, not Phineas. It is Gene who wishes to find a petty motive behind Finny's actions. He suspects Finny of wanting to "finish me for good on the exam," by having him accompany him to a Super Suicide Society meeting, but Finny is without malice. For, he looks at Gene with "an interested, surprised expression. 'You want to study?'....Don't go. It's only a game."
As Gene "was groping for what lay behind his words," he realizes that Finny "had never been jealous of me for a second. Now I[Gene] knew there never was or could have been any rivalry between us. I was not of the same quality as he" (Chapter 4). Gene also reflects, "Perhaps I was stopped by that level of feeling, deeper than thought, which contains the truth."
Gene states that "it was what you had in your heart that counted." His return to Devon as an adult is a return to the sight where he felt an enmity and jealousy of a friend who had none in his heart. Gene cruelly shakes the limb on Finny because of this virtue in Finny as so often people resent others who possess what they themselves do not have, Gene, the adult realizes as he returns to Devon to find his "separate peace."
Finny accuses Gene of trying to be the best in the school and be better than him. He asks him go out with him to the tree with some of his classmates and Gene says that he had to study for some exams. This particular event foreshadows the events at the tree when Finny falls out of the tree due to resentment.