What happened in the tree was no accident. Gene "jounced" the limb, causing Finny to lose his balance, fall, and break his leg. He did not plan to do it, but he did it, and his ensuing guilt drives the novel and helps develop its most profound and troubling theme.
After Finny was released from the infirmary following his injury, he went home to Boston for a while. Gene visits him there and attempts to confess what he had done, but Finny will not allow it. He does not want to talk about what happened. It is only in the novel's conclusion, shortly before Finny's death, that he and Gene speak openly of what had happened in the tree. Finny accepts that Gene had caused him to fall, but he refuses to believe it was done out of hatred:
Something just seized you. It wasn't anything you really felt against me, it wasn't some kind of hate you've felt all along. It wasn't anything personal.
Gene struggles desperately to make Finny believe this was true:
It was just some ignorance inside me, some crazy thing inside me, something blind, that's all it was.
Through his tears, Finny accepts this explanation, saying he understands and believes Gene.
Gene spares Finny from the rest of the truth, the resentment, the anger, the suspicion, and the jealousy he had once felt toward him. The blind ignorance inside Gene, we can infer, was his own capacity for violence. The idea that there is "something ignorant in the human heart" occurs again to Gene when he concludes that it is this "ignorance" that causes war.