Well based on what I have observed, you will find the pebbles only in the mosaic area after the dam is built, the shells on the beach, the beetles in the gong encasement area after the thorns are cleared, and the butterflies all over the place. Hope I helped someone out.

Oh, and I have:
Butterflies: 11/12
Shells: 11/12
Pebbles: 11/12
Beetles: 10/12
so far anyway.