Well pus usually = infection. So unless your vet had already ruled it out, that's the next logical step to take. But since it seems like youve covered that route as you are wanting more possibilities, what did your vet say about the pus previously, did they treat with antibiotics? Did it get better after the antibiotics? If so, how long after? What meds were used? If there's another spot then it would seem like either the antibiotics weren't given long enough or it was the wrong kind.
Could you describe the exact locations on her body and what they look like? Could always be a staph infection.
Does it look like it could have been and infected ingrown quill?
Either way, as I said the pus just points us in the direction of some sort of infection, and only your vet can tell you which type. Secondary infections due to mite damage(or any skin damage for that matter) is not uncommon.