I have a mutated cub, who is a Pie. She shows up in the Falcon Eye list when checking for mutations, which wouldn't be a problem if she went away when I checked her. But she remains there and I keep getting the error that she has a visible mutation. She is named, but the way my caves are organized, she's always on top.

My suggestion is to remove the already mutated cubs from the list, either right away or the first time you check them.