She may have done this accidentally. This is more likely to happen if you have a whelping box without rails placed around the inside of the box. These allow pups to slide under it and escape from being smothered. However, it may be more likely to happen in new moms who aren't sure what to do with puppies. Normally, when she lies on them, their whines should tell her to move away. Healthy puppies with loud voices are more likely to attract mom than weaker, sickly pups. If this is a problem, you may have to separate the pups once they are done nursing and return them every 2-3 hours to nurse again or you can bottle feed them. Make sure they stay warm if removing them/bottle feeding them. Please read how to properly bottle-feed puppies if you choose that route.