fightingbunny
Songster
I have that same coop and I adjusted how the roost bars are so that they were higher up than the nest boxes. The chickens sleep on the roost bars now and do not poop in the nest boxes. I think it also had to do with maturing. Little chicks do not like to roost as much as laying hens perhaps.
https://www.backyardchickens.com/threads/help-hens-roosting-in-nest-boxes.1134399/page-2
https://www.backyardchickens.com/threads/help-hens-roosting-in-nest-boxes.1134399/page-2