I feel your pain! Riley was really bad about it when he was a puppy. We did our best to pick it up immediately. He did "sort of" grow out of it.... I say sort of , because he has an immune disorder and occasionally has to take prednisone. I don't know if you have any experience with a dog on Pred but they think they are starving... So, whenever he on the pred, he will race you to a pile! It is horrible!
I used to have a chow that did it as a puppy and my vet at the time told me to put Adolph meat tenderizer on his food. I just sprinkled a little on the top. Supposedly it tastes good when they are eating it the first time, but doesn't taste good the second time..I don't know if it really works or not, but my Chow did stop even bothering with his poop after about a week of that. I tried it with Riley too though, and he could have cared less.
About the pebbles....I wouldn't be too worried as long as they were small. Riley ATE everything in the house and in the yard when he was a puppy ( i mean everything ) and it always showed back up within a day or two.