This behavior sounds concerning. While it is always best to have mother dog care for her babies, if her you are worried about her harming them, you can hand raise them (this means you will take over the task of bottle feeding them, keeping them warm and helping them eliminate). You would basically treat them like orphaned puppies. The other option is to supervise them when she feeds them every couple of hours and take them away in between ( and doing everything else a mother would do). Please be careful taking them away as some mothers are protective of their puppies. You may need to have somebody distract her or take her out. Please note that mother dogs may accidentally crush them, to prevent this it's important to have a whelping box with "pig rails." If you do not have rails in the whelping box, you may need to stick by the whelping box when they are nursing to make sure they are not smothered and that she doesn't harm them in any way.