One of the early Rife frequency treatments I gave my wife, who has Lyme, resulted in many blisters in her mouth. I am fairly certain it was die off from the Lyme as a result of the treatment.
It did happen one other time, but to a lesser degree, a couple of years later. I started using a different frequency, and apparently it hit some other form of Lyme which had a similar result.
Yours may also be related to die off of Lyme or a virus, near the surface of the mouth. If it is, it should resolve itself in a short time.