The only way you can keep them from doing it is either remove them each night and put them on their roost or block the boxes at night so they can't get into them. Then you have to unblock them after they have gone to sleep or in the morning. I have heard making sure the nest boxes are lower than the roosts helps, but that makes no difference with mine. Three of my last batch of girls love sleeping in the nest boxes even though there is plenty of roost space. I've been blocking the boxes for a couple of weeks now, but if I forget - they are right in them. I wouldn't care but getting the poop out each morning isn't much fun.
Good luck!
