I get them too. On the roof of my mouth and on my inside of my cheeks. That along with ulcers makes for a very sore mouth at times. What I use is plain old salt in warm water. It has antiseptic properties. Not too much though, it can make you sick.
I first used after mouth surgery to clean the stitched area, on the recommendtion of the dental surgeon. I realised then that it would keep my mouth from getting inefected from mouth sores connected to my SLE.
I also use a straw when drinking anything when my mouth is sore.
I hope you get better soon.