[CavyMama]

I would take her to the vet just to be on the safe side but look for a vet not associated with the humane society you got her from. You should get an objective opinion. The brown gunk sounds like it might be dried blood from where she tried to scratch that area. Missing fur is an indication of possible mites. They looked for mites and didn't find any but that doesn't mean they aren't there. Another reason to take her to the vet is that he/she might find some other underlying conditions that were not readily obvious to the humane society.

It's possible the missing fur may have come from a run in with another piggie but it's better to err on the side of caution and get her checked out to make sure she has a clean bill of health.