Mother dog keeps taking puppies out of her nest?

If she has a uterine infection the hormone disruption may be affecting her maternal behaviors. If she is a first time mom, she doesn't really know what she is doing and is learning as she goes. It is possible she wants to move them to a new nest box at this age. Many canids do that to get the pups to an enviroment clean of food scraps, waste, and hatching fleas. It also is an aid in avoiding predators drawn to the smell. Fox farming was revolutionized and pup losses decreased when each pen contained two nestbox houses, one at each end of the pen. The mom could move her pups whenever she felt the need and had a good place to put them. Some dogs like to move puppies also. It will be interesting to see if when it's weaning time she'll regurgitate partially digested food for them. Some GSDs retain this instinctive behavior, and some huskies as well.

Dog Nest

Mother dogs that have recently had puppies will sometimes leave their newborns out of their 'nest.' They are able to smell the puppies' pheromones, and they will be able to tell which ones are weak or not. Sometimes, though they appear strong or stable, they may not be internally. Watch the puppies taken out by the mother carefully.

You should ask the vet and also the organization you are fostering for for more help. Do you know if it is the dog's first litter? She may be stressed, confused, and overwhelmed by the pups. Since it isn't always a certain pup, it doesn't sound like she is trying to get rid of the runt or anything like that. And she is putting them back by herself right? And it isn't like they are old enough for her to be making them more independent yet. Does she seem to want to clean her den when the takes the pups out?

It is normal for a mama to move all of her pups to a new area every so often. She may have the urge to move them but also feels they are safe where they are. As long as she isn't taking one (or two) out of the bed and leaving or ignoring them, this is perfectly normal. Six pups is a normal size litter. As long as she is getting enough to eat and isn't getting too thin she will be able to feed them. Bless you for taking her in and giving her a calm place to nurse her babies.

No need for concern from what you just told us. Its something that different breeds do. Not 100% why but I have my guesses. The only time there should be concern is if the mother stops feeding the pups. Other then that everything should work out in the end.

She is obviously very stressed and trying to hide the puppies, yet isn't quite sure how to do that.

Try and stay away as much as you can and let her settle in.

She also has to stimulate them to go to the bathroom for the first 2-3 weeks by licking them and then if she continues after that it is for keeping the area clean as others said.

On occasion I have seen one ot two of my poodle girls do this. But it was so she could straighten the nesting box up..

In my opinion as long as she is not hurting them and is coming back to retrieve them them she is a good mother.

She's probably a first time mother and never had experience with puppies