If the run is lit and the coop is not, they may be reluctant to leave the light and go into the dark coop. You may need to change the light to inside the coop instead, or put a brighter light inside the coop. Once it becomes habit and automatic for them, you may be able to slowly wean them off the light. Honestly, some groups figure it all out quickly and on their own, and some groups need a lot of assistance until they do.
