Who noticed that the littluns were missing?

I think you are referring to the end of the second chapter of the book, Fire on the mountain. When the fire gets out of control Piggy points out that they don't even know how many littluns there are, let alone if any of them are missing. He then realises that one littlun in particular, a small boy with a mulberry coloured birthmark on his face, is no longer around. The small boy is never seen again, presumably killed by the fire.