This is another one of the big issues that hen owners have to deal with. If you've had hens before, you'll know that they're not the most hygienic of creatures and tend to poop all over the place, even in chicken waterers and around their food sometimes. So yes, they will also poop in their nesting boxes from time to time, but you can help to prevent this kind of behavior by positioning the nests out in the darker corners of the hen house, away from the main areas of activity. You can also take an active role by shooing the hens out of the nests if you notice them pooping or hanging around in the boxes for too long after laying their eggs. In short, you can try to teach your hens that the boxes are only for eggs and nothing else.