My son used to get them, but hasn't for awhile now - I think this is because he regularly eats home made yogurt.
When he did get them, we used oil of oregano, sort of like a mouth wash, or put it directly on the mouth sore as soon as he felt it. It seemed to work like magic and heal it, making it go away before it became big and quite painful. I have tried this too, because I get canker sores when I eat sweets... it did the trick.
Hope you are able to get rid of the sore(s) soon
Mom of 13 year old son diagnosed with Crohn's in Sept 07. Protocol: probiotics, good multi vit, Omega 3, calcium, Boswellia, iron, peppermint oil, weaning off Pentasa (3 per day). Diet: gluten, dairy, egg, and soy free. Always looking for delicious recipes and a better understanding of IBD.