It is possible for a mother to not deliver all her pups. Usually when a pup is retained, a dog does not act normal. They may appear restless, distressed, actively straining, lethargic, non interested in their pups.
However, if your dog is eating, drinking, urinating, nursing her puppies, cleaning them and basically acting normal, she has most likely delivered all her puppies.
If you feel there is a puppy still inside your female, then you should take her to the Vet to be sure. It's a good idea to take her and the pups in anyway for a post whelping checkup to ensure all placentas were delivered as well.
YOU DO NOT remove the mother from the puppies. The mother has to be with them to feed, clean and take care of them. As for the litle one, as long as it is nursing on mom, it should be OK. There is usually a runt in every litter.
The following website gives detailed information on every aspect of whelping.
I hope you find this information helpful.