It turns out these don't mark a collectable to be picked up -- if you do a little twirl on them, a coin pops out. It's just a neat little thing.

Until I broke down and looked this information up, I had been accumulating a compounding sense of dread that I'd be expected to remember where all of these pebbles were later. I don't think modern games are generally that cruel anymore, but I still expect them to be. Some wounds never heal.