"You can toss it or place it as a marker."Pebbles are one of the usable Items in Yomawari: Night Alone.
Pebbles can be can found as sparkling light on the ground when exposed by the flashlight or inside garbage bags and trash cans. They can be found anywhere throughout the whole map.
The Pebbles main purpose is to distract dangerous Spirits in order for the Protagonist to sneak past them.
It also had an important purpose for teaching the Protagonist the controls of the game at the opening, which sadly, was responsible for getting Poro run over by a truck.