What can cause pain after having a root canal?

Inflammation . . . .: After a tooth has been treated with a root canal, there can be inflammation which can result in pain/discomfort. The ligament fibers of the tooth that anchor it into bone can literally swell and cause the whole outside of the tooth to become sore even though the nerve inside has been removed. Also, the injection sites where you were anesthetized can be sore as well.

Inflammation: There can be a lot going on here. If you feel pain after a root canal you should see the dentist that did the root canal. Very simplistically in the absence of other causes the classical reasons for a "flare up" are chemical, microbial, or mechanical trauma to the tissues around the tooth resulting in short term discomfort.