You, actually, didn't tell ccleaner to skip firefox; you told it not to warn you that firefox is open. Your firefox skips cleaning because firefox is open or has left something still running. There is the option to return those warnings in settings (I think it's called "show warnings" but I don't have access to a pc right now).
To stop ccleaner from skipping firefox, though, you'll need to figure out why firefox is still running in background when you use ccleaner.