What message do you see in the kid's action line?

If it is being treated as a new collectible it will say something like "Collecting a new item!', if it is a duplicate it will say 'Collecting an item for the scientists'. I don't have the game on this PC and I'm relying on memory, so the wording may be slightly different. You should also see the tech points tick over by 100 points when the kid enters the hut. If the pebble definitely does not show in your collectibles screen after the kid has delivered it to the hut it does sound like a glitch, although I've never seen anything like this reported before.