Honey bees will not be a problem. Various wasps and hornets are another thing altogether, though I have only had them build nests on the outside of the coop. Whether or not that becomes a problem will depend on the species.
I'm guessing the OP probably means wasps. I keep an old broom in the shed attached to my coop. When I see them starting to build nests, I swat them down. They're usually on the outside, but I occasionally have to take one down inside. I've never had honey bees move into the coop, and we have a hive right on the back wall of it. I occasionally find them in the chicken feed (usually early Spring, even before we got our own bees) and very often find them at the chickens waterers. They don't bother the birds and the birds don't bother them