Small holes and left over shells sounds like mice. When my chickens eat and egg, they eat absolutely everything. The only evidence left behind might be a little wet spot. Now, when I had a mouse problem, I would find left over shells in the nests, on the floor, I even found one on the roost. Sometimes they'd be cracked in half, other times they'd just have a whole chewed into them but the insides were always gone. Make sure you collect up all you're eggs every night if you aren't already. Put up your feed as well, give them nothing to eat if you can help it. And TRAP, TRAP, TRAP until you can't catch anymore. I used a bucket trap bc I didn't want to put poisons or snap traps near my chickens. It worked great. I'd set it at night when I closed up and pit it away in the morning before I let everyone out. To make the bucket trap you fill a 5 gallon bucket 1/3 way full with water. Cover the entire water surface with sunflower seeds (no salt, in the shell). Provide the mice with an access ramp. They jump in thinking they've found themselves a bucket of seed and never come back out. Good luck!