Hair Loss Uri and bald spot by mouth

I purchased my first two guinea pigs from a pet store two weeks ago before realizing there were other options. We'll now I love them and would never return them. We've built them a c&c cage with fleece, they get unlimited hay, a variety of cavy friendly veggies, fresh water, a vitamin c supplement everyday, and high quality pellets. I feel I am doing everything I should be doing yet I'm still having problems. A fee days ago I noticed my Ellie sneezing quite a bit. I took her and her sister munchkin to the vet who preformed a fecal test and checked them both out thoroughly. She gave me baytril and doxy for antibiotics for two weeks. They seem to be sneezing less and are still active and eating. My biggest concern now is they are both losing hair by their mouths. The piggies are still young and don't exactly love taking their meds and the first few times I missed a little by their mouths I'm basically wondering if the medication could be causing hair loss. The skin doesn't seem to be irritated, no redness or scabbing. Just missing hair right by the mouth. I'd really appreciate any advice I plan on calling the vet tomorrow as well.