Awe that's a real bummer!!! No offense to your breeder, but $100 off is a rip off for a known issue. It will possibly be $500 for surgery when your baby is old enough to get it done, and all the ointments and vet visit costs before and after. It's also possible for it to go away completely but unlikely.
No it's not a major issue but they can sometimes get infected and you will want to wait a little if possible to have the surgery done. If one has pooped out at this young of an age it's likely they both will.
They can be caused by an eye injury (which is very possible in a rowdy litter of pups) but usually it's due to the strength of the third eyelid muscle.
I have never heard of them being caused by a parasite.
Check out the article on cherry eye too.
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