You can find the answer to this fairly early in Chapter 4. It is about 4 pages in to the chapter.
The reason that Maurice feels guilty about this is that he has some remaning memories of civilization and what civilized people are supposed to act like. He remembers that he once got in trouble for doing the same thing to a younger kid's eyes back in England.
So it is a memory of what the rules are that make Maurice guilty. This shows that he still has a conscience and has not become a real savage yet.
In Chapter 4, a few of the littluns are enjoying themselves as they build sand castles by the edge of the water. As the littluns are kneeling in the sand, Roger and Maurice run out of the forest and begin kicking down their sand castles. After Maurice kicks down one of the castles, Percival begins to whimper because Maurice had kicked sand in his eye. Golding writes that in Maurice's other life, he would have been chastised by his parents or an adult for kicking sand in a younger boy's eye. However, Maurice pauses and feels the "unease of wrongdoing." He even comes up with an excuse in the back of his mind before he continues to run away. The reason Maurice feels guilty about kicking sand in Percival's eye is because he is still influenced by civilization. The boys have not been alone on the island long enough to completely dismiss their past. The rules, laws, and taboos of civilization affect Maurice to the point that he feels guilty. As the novel progresses, the boys completely descend into savagery and are not impacted by the laws, rules, and taboos of civilization.