I believe you are referring to Roger who throws stone near the Henry instead of at him. This occurs because “Roger’s arm was conditioned by a civilization that knew nothing of him and was in ruins.” In other words, Roger is still being influenced by civilization and has not yet turned into the savage he will become. Henry, himself, thinks it's a joke and looks for Roger, but Roger hides and no one really notices the "strange pleasure" Roger took in throwing the rocks. This event foreshadows a more horrible event at the end of the novel.
Roger has not yet completely forgotten the rules and laws of his old life in Britain. Note the lines "...there was a space round Henry, perhaps six yards in diameter, into which he dare not throw. Here, invisible yet strong, was the taboo of old life. Round the squatting child was the protection of parents and school and policemen and the law." (pg 65) Roger is so used to the laws that were enforced upon him in his old life, that he has not yet broken free of them to follow his own morals. It is almost out of habit that he does not throw the stones. He probably still feels a bit guilty as well, because in Britain he was taught as a child that throwing stones was wrong.