What do your facilities look like? How big is your coop and run and is the run open to them when this happens? How much age difference is there between your chickens?
There is obviously a lot I don’t know about your situation, so I can only guess. One of the ways chickens have learned to live together in a flock is when there is a conflict the weaker run away from the stronger or just avoid them to start with. A more mature hen outranks less mature chickens in the pecking order. Sometimes the higher ranking hen can be pretty strong in enforcing those pecking order rights if a less mature chicken invades her personal space. Some will even go out of their way to be brutish to the less mature chickens. That’s why when you have different ages of chicks, the younger ones seem to form their own flock and stay away from the older chickens. If you don’t have enough room for them to physically separate, they look for places to hide.
It is really common when I integrate younger chickens to find the young ones up on the roost in the morning when I go down to let them out. They are up on the roosts avoiding the older chickens on the floor. A lot of the time they hide under my nests, which are fairly low so they make a good hiding place. I’m guessing yours are hiding in the nests.
So what can you do? You obviously can’t block off the nests if you have a hen laying. Give them more room if you can, especially with separation. If the hen is in the run, the chicks will probably be in the coop, but not necessarily hiding in the nests. If she is in the coop, they can go to the run to get away.
Provide more hiding spaces, things for them to get under or behind so the hen can’t see them. Something about 5” to 6” off the coop floor looks real safe to them. Or something fairly close to a wall so they can get out of her site. Try not to trap them though. Give them an escape route if she attacks.
If you roosts are low enough that the hen can reach up and peck their feet, the roosts are not a safe place. But if you provide perches high enough either in the coop or run, they may start to use those to avoid her. One risk with perches in the run is that the younger ones may start to roost out there at night to avoid having to roost close to the hen.
Eventually the younger ones will mature enough to force their own way in the pecking order and this problem will go away. Usually with mine this is when they start to lay, but some take even longer.
Remember, all this is just a guess. Good luck!
in the pictures.... You are missing a roost behind ... We can't see it but we have 12 feet total...
