Hello and Welcome to BYC! Like everybody said, the broodys especially will move eggs around in the nests, and in communal nest boxes sometimes there is a lot of stealing and rearranging going on. I am not sure what the distance is from the coop to the nest boxes, but if it doesn't seem likely that a chicken could move an egg from one to the other, you might want to consider if you have something else eating or stealing eggs from the coop floor.