I am glad you took the male puppy back to the breeders. If he was only 9 weeks, and you had him for three, then he was only 6 weeks. You are absolutely correct, he was way too young to be away from his mother and littermates. 12 weeks is the reccomended age for a Yorkie puppy to leave . my concern is why take anther pup at this age? When you have already been through this with the male? He could have easily died. Perhaps, waiting anther 2 1/2 weeks would have been a lot safer, and better decision . I know it is difficult to wait until a puppy is old enough, however, as you know, it makes all the difference in the world.
I hope that the little female will be ok. And i believe that your going to be in contact with the breeder, and know the signs to look out for.