As she just delivered she probably is very tired. You can carefully put new bedding down over the messes as you will not be able to change the bedding unless molly leaves the nest to eat you will have to throw out the bedding anyway i have found that if you happen to be there when a kitten messes maybe putting the bottom end to Molly will give her the idea to clean up. The messes on the bedding will have to wait until later.