
It is possible that even with 9 puppies, she's just not able to take in all the food she's getting. And as usual most dogs will need to have a BM for as many meals they have, BUT the stools should be normal. However having said that, even if this is 2 weeks on now, if she took in a lot of the placenta, this is very rich and can upset the dig.system. Bitches in the wild eat this, as they can't go hunting for some time, to sustain them.
Also have you wormed her yet because by 2 weeks, the puppies should be getting their first worming, and her at the same time.

Just realised this latest post is a few weeks on from the first

Natural yogurt should help clear up uncomplicated tummy upsets for sure - and if you can source goats yogurt, so much the better. Giving her milk could cause a digestive upset too.
In general, it's the suckling that stimulates lactation. So increased food alone shouldn't. I have to say that despite my best efforts, some of my bitches would give their ALL to their puppies and end up, just at the time when people come to see the litter, looking like two boards clapped together. And their coats can drop too. Don't panic. And don't be persuaded to pile in an abnormal amount of food either. As she starts to get out on her normal exercise, and eating up better, her condition should come back fast.