Wondering if you have ulcers, too? I had ulcers and what looked like blood blisters in my mouth prior to diagnosis with celiac and it felt like I was eating crushed glass at mealtimes. Soooo painful. I started drinking a fizzy vitamin drink which was v. rich in B12 and C vitamins and they went. Do you know what your B12 levels are like... might be related? Mind you, I also had low blood iron and I gather that can cause them too. Just a thought.
I had canker sore type things before the blisters. They would go away after 3 days or so. I couldn't eat even 2 cherry tomatoes without getting them. Never had b12 checked but yes to low iron. My feretin levels were still below normal despite a prescription iron supplement I'd been on for three months.