Maybe one of the breeders on the forum will respond, but I do know that certain foods will cause staining. Maybe the mother's milk, in this case, is causing staining. I know that many things a mother eats are carried through into her milk. Maybe something in her diet is causing it. Since it isn't dangerous or a sign of ill health, the breeder may just choose to ignore it, knowing it is likely to go away once the puppies are weaned.
Have you talked to your breeder about your concerns? IMO, it's really important to develop a good, trusting, working relationship with your breeder. If you have a good relationship with her, and develop a feeling of trust, she can be a wonderful resource to you in the months to come. I know that there are a lot of scary stories on this forum about things that have gone wrong when people have purchased puppies from less than reputable sources. But hopefully that is not true in your case. (I don't know the breeder, but the fact that one of our forum members went back to her four times for puppies says a lot to me)
It can be easy to read all these stories and start mistrusting everything a breeder says. There are a lot of really GOOD breeders out there too, who care deeply about their puppies, and do everything they can to make sure they are healthy, happy and placed in wonderful homes. It would be a shame if you missed out on developing a trusting relationship with your breeder based on what you've read about not-so-good breeders. At this point, I think you are committed to this puppy. As I see it, you have two options. Either start to build a trusting relationship with her or cut your losses, even if it means forfeiting a deposit, and find another breeder whom you CAN trust. Your little guy looks like a darling, and you should be enjoying this period of anticipation rather than worrying the time away!