You can get things like that in your mouth for a lot of reasons. That said, in your shoes I would go see a doctor. The problem would not be caused by the birth control (if you are talking about the pill) but who knows if it is an STD or something totally else; for example, one time I got gum boils from lack of vitamins. See the doc, get swabbed, and find out if it's a cold virus, or an STD, or strep, or the flu, or what.
Do ask your doctor about your birth control being involved for the issues of your mouth. I suspect they are indeed related.