I have 12 chickens. I've raised them from day 1. They have a coop and a 10' X 10' enclosed run (for during the day while I'm at work) then they free range all other times. They ALWAYS go into the coop right around 8:00-8:30 every night. For the past two nights, one lone chicken roosts up on top of the run. Tonight I walked right over, picked her up and placed her in the run (she then walked over and got in the coop.) Is there anything I should be concerned about?
I'd concerned that a hawk or owl will pick her off the top of the run. I've had some of my better flyers do that - roost on the top of the run - I clipped the feathers on one wing and that put an end to that.
How big is your coop? That's a pretty small run for 12 chickens to spend the day in, if she is at the bottom of the pecking order she may be getting bullied when it's time to roost so she doesn't want to go in. I have a couple of bantams that roost on top of my two coops but they are inside a closed barn at night so I let them be.