They have a roost in the coop that they don't like at all, and one in the run that they love but they may feel too exposed on? Also, I have looked around in the run for aome kind of little animal and haven't found one, but the run is right up aganst a shed, maybe something crawls under there...
At dusk, my approx 15 week old pullets mill around in their run, very agitated. They are trying to "escape" (impossible) and sticking their necks trough the wire, flying at the roof, etc. Its very strange! Then when it gets dark they go to bed in their coop.