Gene decides, after the beach trip with Finny, that Finny is trying to sabotage his academic success. What triggers this is a conversation the two have after Gene fails his trigonometry test because of the beach time. Finny accuses him of working too hard and tells him he needs to lighten up. He informs Gene that he is too competitive, saying:

You want to be head of the class, valedictorian, so you can make a speech on Graduation Day—in Latin or something boring like that probably—and be the boy wonder of the school. I know you.

Gene outwardly denies this, but inwardly admits it is true. He does want to be head of class because it will make him "even" with Finny, who is sure to win all the athletic awards. All of a sudden Gene, remembering that the prep school is a "jungle" where it is impossible to trust anyone, decides that Finny is just pretending to be his friend in order to derail him from success, "he minded, despised the possibility that I might be the head of the school."

All of this tells us much more about Gene's distrustful, competitive nature than it does about Finny. As Gene later realizes, he projected his own fears and "shadow" on his friend. Finny did genuinely want Gene to enjoy life and didn't have any interest in sabotaging him. Gene, of course, feels bad about this later.

After the trip to the beach, Gene flunks a test because he spent his study time at the beach instead of in his room.  When he and Finny talk about how much Gene studies, Gene begins to suspect that Finny is trying to keep him from studying in order to make sure that Gene doesn't overshadow Finny academically.  Gene wants to be valedictorian so he can prove he is just as good as Finny is at something, so he believes Finny is trying to sabotage his studies with trips to the beach, club meetings, blitzball, etc.  His own jealousy of Finny leads him to this conclusion, even though Finny never directly says anything to prove Gene's theory.  This all adds to Gene's guilt later in the story when he figures out that Finny was just trying to be a good friend all along.

In A Separate Peace, after the overnight trip to the beach, what does Gene decide Finny is trying to do to him?What leads Gene to this conclusion? How does Gene feel when he realizes he is wrong?

After Gene and Finny return from their overnight trip to the beach, Gene concludes that Finny is trying to deliberately sabotage his grades by keeping him too busy and distracted to study.  He decides this after he fails his trigonometry test, "the first test (he) had ever flunked".  Because Finny had insisted that they take the trip to the beach and blithely overlooked every protest Gene had made that he had to study, Gene had not been able to even look at the subject matter the night before.  Finny's endless diversions continue even after Gene fails the test with the insistence that he take part in blitzball and the activities of the Super Suicide Society.  Angry and frustrated, Gene thinks about their situation and concludes that Finny is jealous of him, and bitterly competitive - because while Gene is

"more and more certainly becoming the best student in the school; Phineas (is) without question the best athlete, so in that way (they are) even..but while (Finny is) a very poor student (Gene is) a pretty good athlete, and when everything (is) thrown into the scales they (will) in the end tilt definitely toward (Gene)".

In Gene's mind now, Finny is trecherously trying to make him (Gene) do poorly academically so that he (Finny) will be the best overall in school.

Gene finally gets through to Finny when he vehemently protests that he can't attend the latest meeting of the Suicide Society because his grades are being ruined.  Finny inexplicably listens this time, regarding Gene "with an interested, surprised expression".  He tells Gene not to go, explaining simply that he had thought Gene did not need to study, that things "just came to (him)", and he humbly denigrates his own academic ability in comparison to Gene's great intelligence.  At this point, Gene is thoroughly confused, and deeply resentful, in the throes of "new dimensions of isolation".  On the one hand, he feels guilty for ever having doubted Finny's motives, and is in awe at Finny's nobility; Gene feels he is "not of the same quality as he".  On the other hand, this sense that Finny really is so much better than him infuriates Gene, and he goes to the Suicide Society meeting at his own insistence, feeling confused and deeply resentful (Chapter 4).