If your chickens go out to a run or to free-range and are not in the coop all day, I'm gonna assume that she is messing up the nest box by roosting on it at night.
Make sure your nest boxes are lower than your roosts and make sure you have enough roosts for everybody. It may be necessary to go in the coop at night for a few nights and move the hen from the nest box and put her on a roost. It'll usually click in their heads to use the roosts, but it can take several days of moving her at night.
None of the hens are sleeping in the nesting boxes. One goes in there during the day, probably when she lays her egg, and then poops in the box on the eggs. She has done this three times already. As I am currently working out of state, the hens do not get let out until the afternoon when a friend comes to collect the eggs and let them free range for a few hours. WHen it gets dark he checks on them before closing up the coop for the night. They are all on the roosts at that time. I will be home in one week, and they will then be able to be out in the run from dawn till dark. Maybe then she will stop.
Ha! I bet she is telling you she doesn't like the schedule being stuck inside! I don't know of a solution short of closing off most of the nesting boxes. Maybe others would kick out the offender when they needed to lay.....
Sorry for the yucky problem. I have worried about this happening.
i have a kind of odd thing going on in mine right now...they are using only one nest box as a toilet. there's barely (although, yes, some) any poop anywhere else in the coop. they are using the nest box closest the door as a ...well, for lack of better terms, a cat box.