I think you need to block their access to the nest boxes till they get nearly old enough to lay, like around 16 to 18 weeks. Otherwise, they will keep messing in them.
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I just read they are 9 weeks, they are still fairly young. If you don't have older hens, block the nest boxes and let them sleep on the ground. My youngest are around 12 weeks and just started jumping up on the roosts in the run. I've done this before and it does take time before they get it. My roosts are 5ft high in the coop and 2 feet high in the run. I can't block my nest boxes since I have older hens and some lay right away in the morning. I add new chicks every year, so I'm always integrating. Don't give up.I did that tonight, left them alone for a few minutes- one had jumped down so Iput her back up. She jumped off again, and so did all of the others, but one, who probably jumped down after I left. Day 1- fail.