I just experienced this same thing. The bitch is overprotective of her pups. I had my bitch inside the house in a 800 kennel (Extra large) and I slept by her day and night for 4 days straight constantly rearranging her when she laid on them. I myself scolded her a bit in my impatience, being very seep deprived.
I believe it helped her understand that I was not happy with her plopping herself on them.
Eventually when she would plop down on them and they cried out as soon as she heard my sigh and saw me getting up she began to arrange herself off of her puppies. If the litter is important to you like mine was to me you'll do whatever it takes to raise them all. I lost 1 pup on the second day but it was weak from the start. All of the remaining 6 are doing great and almost 12 weeks old now.
Good luck!
S_B