Yes. I have found 3 small holes (quarter-sized) since June. No other chicks were lost. I believe I may have a hungry mouse looking for a meal. Why the hens don't kill it is beyond me. Before building the coop, I lined the perimeter with patio stones (they go down 16-18"), filled it with sand, & then built the frame of the run. After that, we used hardware cloth.
It's possible the stones have shifted leaving gaps. Are chipmunks, mice, & rats harmful to poultry? I do not believe I had a weasel b/c it was only one loss.
Mice and chipmunks should be no problem, but rats may harm young poultry. I would guess that rats are not the case with you if they are small holes.
Some chickens are really good mousers, like my neighbors- they seem to catch one every other day or so - none of mine have caught one yet (that I know of) but I know they're around!