Tracing many of themes of "Lord of the Flies" marks out the downward trajectory from civilised reason to savagery and choas which the book as a whole marks - and Roger's stone throwing is no difference.
When throwing stones at Henry, Roger (who innately seems to enjoy causing pain to the other boys) throws only to miss.
...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 the old life. Round the squatting child was the protection of parents and school and policemen and the law. Roger's arm was conditioned by a civilization that knew nothing of him and was in ruins.
Of course, as the civilisation breaks down, Roger's stone-throwing becomes to hit, and eventually, to kill: this is from shortly before Piggy's death:
Someone was throwing stones: Roger was dropping them, his one hand still on the lever.
And of course, Piggy's death eventually is caused by a (symbolically as well as literally) much larger stone, propelled by Roger: a symbol of the way Roger's sadism has expanded from a suppressed mischief into a terrifying, dominating force.