No it does not sound right and I suspect the remaining puppy either was not tested for parvo or has not yet broken with it.
Another possibility is if the breeder gave a vaccination and your pup isn't showing any signs of disease the vet's test might have picked up the parvo from the vaccine in a standard test.
However a puppy can test negative for the disease and have it the next day.
You can read more here
http://www.marvistavet.com/html/body_diagnosis_of_parvovirus.html
If your puppy is sick and you've had it less then three days then you got it sick. There is a 3-7 day incubation period for this disease.
If your pup is showing signs and you do not want to return the puppy you can see if Tamiflu will help the pup through the disease.
www.marvistavet.com/html/body_oseltamivir.html
Hope this helps you!
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