I have had that issue as well, they want to sleep in the nesting box and it's full of poop the next morning. A few times I have gone out after dark and thrown them out of the box, and eventually I took an old pillow I didn't use anymore and just shoved it in there near night time to fill in the box so they could not get into it, then in the morning when I clean the poop out of the main area and feed them, take the pillow out so they can get in to lay their eggs. Generally only takes a few days of this and they get the idea to sleep on the roost.
Aaron