What Aart said.
Are the roosts higher than the nests? Chickens normally like to sleep on the highest place available. But there can be exceptions.
The normal age for my brooder raised chicks to transition from sleeping on the coop floor to the roosts is usually around 10 to 12 weeks. I have had some do that at 5 weeks and some a whole lot later, but yours are ahead of my normal age. But when they are transitioning from the floor to the roosts, they may sleep on things part way, like nests. Usually they move on but occasionally some get stuck there.
They are often creatures of habit. That’s why closing off the nests until they get used to sleeping on the roosts is a good idea if you can do it. I can’t because I have older laying hens in my flock, so I put a separate roost higher than the nests but lower than the main roosts and off to the side to give them a place to go that is not the nests. Occasionally I have to move some from the nests to that roost after it’s dark before they get in that habit. I’ve got eight 12-week olds sleeping on that training roost right now.
I don’t know how much roost space you have either. In tractors space, weight, and even height can be limited. I find mine are most vicious to each other when on the roosts settling down for the night. Where they sleep is a pecking order thing and some of my older chickens can be pretty brutal to younger chicks when settling down. That’s the real purpose of my extra roost, to give those chicks a safe place to go that is not my nests. I notice your cockerel is a bit older than the pullets. At that age he may be keeping them off the main roosts, especially if space is tight. Eventually he will mature and stop that if that really is happening, but it may take time. It’s also possible it’sone of the other pullets being a brute on the roosts and not the cockerel, but because of the age difference I’d bet on the cockerel.
I’ve had the problem with chickens scratching out the bedding or even fake eggs. That problem was solved as Aart suggested, by raising the lip to 4” or 5” to keep the bedding in. Chickens just scratch, that’s what they do. When a hen is settling in a nest to lay her egg, she often rearranges the bedding. When they are just looking around, they scratch. I’d look at the lip height.
When pullets start to lay, it’s possible they will drop their first egg or two about anywhere. Most pullets get it right from the start but several do have problems. I think it helps with mine that I have older hens that show them where to lay. Fake eggs do help. But once they gain control of that process, they look for a safe place to lay that egg. As they are creatures of habit, once they lay that first controlled egg somewhere, it can be difficult to retrain them to use the nests. Pullets often start to search for a safe place to lay that egg about a week before they lay that egg. Your cockerel is too young for this but some roosters will even help a pullet look for an acceptable place to lay.
I want the nests open before they start to lay. The earliest I’ve ever had a pullet start to lay was 16 weeks age. That’s pretty rare, usually it is weeks later. But my goal to get the nests opened up is 16 weeks. If I’m going to have trouble with chickens sleeping in the nests I want to know it before I start getting poopy eggs so I can work on the problem.
What I suggest is that you block off the nests so they get used to sleeping somewhere else. If your roosts are not higher than the nests, either raise the roosts or lower the nests. If roost space is tight, try to put up more roost space if you can. If some seem to get stuck at nest level or below, try moving them at night after it is dark to where you want them to roost.
I used to have a tractor. I know how limiting space and weight can be, especially if you move them by hand. Your number of chickens is kind of getting at the upper limit of how many you can house with a hand-movable tractor unless you do something like use electric netting or maybe guard dogs to give them more room. My tractor was actually in two pieces that could be moved separately but linked together after they were moved so they could move back and forth. I gave up on the tractor idea because I had to move it so often even with the extra space the two parts gave me. As long as they have access, they don’t need to sleep where they lay eggs. If you are committed to the tractor idea and limited by space and weight, you might consider building a separate module you can link together but create more space, especially higher space, then train them to sleep where you want them to.
Good luck with it. You can work through it but in a tractor especially you can have challenges.
