Ectoparasites (External Parasites)
Cryptocaryon irritans, Amyloodinium (Oodinium) ocellatum, Brooklynella hostilis, parasitic crustaceans, gill flukes, Glugea, etc.
Symptoms:
visible parasites upon examination manifested as white spots, ulcerations, blisters, etc.
Sounds like your pony is displaying an ulceration. You may want to look at Flesh Erosion disease also. I don't think the bubble diseases manifest in that way.
Brian