This is a problem that happens every single time I introduce youngsters into the hen house. They clump together in groups and jam themselves in the nest boxes. They poop in them all night and I hate gathering poopy eggs! But I noticed that they only ever roost in the top row of boxes (I have an upper row and lower row). This time I propped a piece of cardboard over the top boxes and blocked them out. The hens could still get into the lower boxes to lay eggs. This solved the problem and when I took the cardboard out 10 days later, no one roosted in the nest box.
Another thing, at night make sure your hen house is absolutely dark. This cuts down on the roost bullying a bit. If they can see each other at all, they pick and shove even worse. There is lots of room on my roosts, and the roosts are higher than the nest boxes, and I think it's just a problem of grumpy old hens not sharing with newcomers. Block them out, make the hen house dark and cross your fingers.