Why doesn't Gene respond to Finny's affirmation of their friendship at the end of chapter 3? A Separate Peace by John Knowles
Chapter 3 of A Separate Peace is a clear foreshadowing of the rift (and worse) which is to come between Gene and Finny. The two of them have sneaked off the beach for the day, and it turns into a night. Gene is unable to study for his exam; and, because his grades are supremely important to him, Gene is angry at Finny. Finny has virtually no clue how Gene is seething on the inside, assuming his feelings of friendship and trust are reciprocated. At the end of this chapter, Finny tells Gene that he's his best friend. The response is silence. Gene says:
I should have told him then that he was my best friend also and rounded off what he had said. I started to; I nearly did. But something held me back. Perhaps I was stopped by that level of feeling, deeper than thought, which contains the truth.
The answer to your question is simple: Gene doesn't respond to him because he clearly does not, at that moment anyway, see Finny as his friend. Even worse, Gene sees him as an insidious enemy--which is the only way to explain the events which happen next.