No, they can't refuse to pay her. If she worked, they HAVE to pay her. The law is very clear on that. If they don't pay her, your daughter may contact your State's Department of Labor and file a complaint. (It could be the boss is just trying to get her attention by putting a scare into her though.)
What they can do is discipline your daughter for failing to follow timekeeping procedures, including terminating her employment should they wish. I suggest she start remembering to punch in and out.