[LunarBerry]

O.o I must say that doesn't sound right. Maybe it's just my experience, but all my doggies had shots in their rear not front/shoulders (I only know of "up the nose" for certain vaccines). If the scab was that bad to go to the vet, I'm assuming it was a fair size too. I also don't see how that could be from the "shots", but since it was a puppy mill I can guess the needles/place they were kept wasn't clean/sterile enough. Either way it does sound that she needed antibiotics anyways. Better safe than sorry. I guess you only have two choices, wait it out and let them check her again or find another vet for a different opinion.
Not saying they are terrible vets, I just find it odd they say it's from her last shots when with a sore it could also come from rubbing or long term pressure on a spot that could come from being caged. And if she is from a puppy mill, you can't be 100% sure she has even had any or all shots. Again, I could be wrong but that's just my opinion. ^^;