I'd look constantly for puppy poop and get it out of there asap before she eats it. It is ok for the first few weeks, but they will be pooping more and more often and it gets to be too much and may make her sick. Trust me, when she gets the runs all through the pen and it is all over the pups, you will be sick. They eat it to "hide evidence" of having pups. It is just their instinct to protect and she doesn't understand that she isn't in the wild and there are no "predators" after her babies. Once you start "collecting" it on your own, hopefully she will get out of the habit of cleaning up so nicely

. I put a pee pad on one end of the pen and at less than 3 weeks the pups will find their way over there to pee.