Aw I am sorry. I know how you feel. I am waiting to bring Julia Rose home too. It is good that the breeder said No. Extra time with the Mama dog won't hurt the pup at all. I am not giving a medical reason this happened. Medical stuff is not my area of expertise
But just want to mention a few things, Cocsidious can lay dormant then flair up when puppies are weaned, or get stressed. It is treatable and requires medication. IMO it is better for the pup to stay with the Mama dog if this is the problem. Going to a new home is always stressful. Doggy flu, and many other minor things can cause runny poop. Be glad that your breeder is working with her Vet to get the puppies healthy before they go to new homes.