In this case we are discussing the river washed stones or "cobbles" that are often used below trees and over exposed roots. An easy solution to a decorative solution for an area that plants cannot root due to tree roots and compacted soil. The problem arises as the cobbles get filled in with leaves and debris which breaks down and forms soil over time. This traps moisture at the crown (where the trunk stops and the roots begin) of the tree. The crown actually needs to breath and the trapped moisture encourages the growth of fungus and a place for insects to lay eggs.
This problem became apparent after a few years of installing these stones and enough accumulation of leaves and soil had filled in the crevices of the stones. Please pull the stones away from the tree crown by about 4-6". Use a blower to clean out the stones around the crown and over the exposed tree roots, which also have bark on them. I do this aobut once per month. It does not hurt to remove stones every 5 years or so and rake off excess soil that has been formed, and then replace the stones.
In general avoid building soil up over the crowns of trees and root masses as this can cause crown rot and kill the trees.
Just a heads up to protect our trees!