Canker sores are not bacterial in nature. They are not specifically viral either, and have nothing to do with STD's, such as HPV. Canker sores themselves are generally immune system based from what I've been told by my doctors if they are a common occurrence; and you are more likely to get them if you are genetically predisposed to get them. I agree with MildlyInterestedYetHopelessyConfused. Changes in pH can spur canker sores to show up. Also, canker sores can be caused by agitation in your mouth, sucking, etc. Which, if you gave head, is essentially what went on. There are various types of canker sores. From what I've found out through research and medical inquiry, it's not because your boyfriend is 'unclean' or the general 'cleanliness' of your mouth. No worries there.
Canker sores can happen for the most benign reasons: tooth paste, citrus juice, or a dental apparatus... It could be possible that you had a canker sore 'in the making', gave head, and it showed up, and you are associating it with oral sex. I'd say, pay attention to whether you get a canker sore next time you give head; the sucking motion could be the cause. Otherwise, it's probably just a canker sore that happened to surface shortly after this incident. I suggest rinsing your mouth with warm salty water a few times a day..
If this actually isn't a canker sore we are talking about and it starts to 'crust' over, then see your doctor. But, my guess... probably just a canker sore. Go on the internet to see the different types of canker sores to double check.
If I recall, canker sores are bacterial in nature. I would tell him to WASH before you do this again.
It may just be coincidence. Since semen is basic in pH and canker sores are caused by too much acid, it's probably not the oral that caused it. Been eating lots of citrus lately? That could be it.