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.
Follow along with the video below to see how to install our site as a web app on your home screen.
Note: This feature may not be available in some browsers.
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.. Keep at it and they will learn. I had to kick my flock of 17 outside the coop and sleep on the roosts in the run since the coop was 100F. We are having a horrid heat spell. Our run is very secure though with welded wire and hardware cloth, so nothing can get through. I wish they'd automatically sleep outside when it's this hot since its 10-20 degrees cooler outside at night. Before I go to bed, I open the door to the coop, so they can lay in the morning. Good luck! I know it's a pain, but they will learn.. Chickens are pretty awesome pets and depending on the breed(very few are skittish), they become very friendly. Mine jump on my back and shoulders every single time I clean out the coop and run.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.