I honestly have no idea, when I quit smoking I never had that problem.
It probably has to do with the concept of nicotine withdrawal, you running really low on it, and your body is trying to cope with it, which increases stress (when i quit, i got extremely mad over really stupid stuff), and stress is a common trigger of canker sores (HSV Type 1).
Other than that, smoking is bad for the tissue on your mouth, it can cause mouth cancer, just like chewing can, and your body might just be fighting off some irritants in your mouth, which again causes stress.