It's common for eggs to get mixed up, moved, or otherwise disturbed when a hen is sitting on eggs in the coop with the others. The broody will also probably return to the wrong nest sometimes, and when she is sitting on the right one, another may climb in the nest with her and lay. They really do best, IMO, if isolated during the setting period, where they won't be bothered and can set in peace. You need something like a large dog crate, big enough to hold food and water, and still give the broody a little space to walk around each day for a little while.
Some people do let a broody stay with the flock in spite of the problems. It helps to mark the eggs to be hatched with a Sharpie so you can rearrange them as needed. You will probably get fewer chicks this way, but plenty of chicks have hatched this way, too.