This looks like some form of contact dermatitis. The question is what she came into contact with.
You guys are fairly active, so my bet is she encountered some bugs..they're still active in NY, especially the last few weeks when it's been so unseasonably warm. It's interesting the vet prescribed antibiotics, did s/he think they were infected? Typically it's best to not medicate unless there's active infection, especially with younger dogs whose immune systems aren't fully developed.
If they're scabbing, try a little Aquaphor jelly on them, it'll keep them moist and reduce the chances of scarring, which means bald spots..yikes!