First, the limit was made for that particular story, not from the get go.
Second, If I recall, the twelve limit was not a natural limit, it was imposed by the Timelords (probably to stop a timelord from becoming a demi-god). Now that the Timelords are gone, the machination that limits the regens may be gone, but the Doctor may not know this, so 13 may think that's the last one. The 507 that 11 told Clyde (Sarah Jane) should/could be ignored. 13 dies, regens, surprised/shocked/tickled/mad that he regenerated (depending on the personality of 14).
In an unrelated topic, every time I go to subscribe to a thread, I think I see Marge Simpson.