He apparently doesn't count as a Doctor basically because he and the other Doctors say he isn't one of them. He was credited as The War Doctor, so... apparently that's his name.
That said, in another interview, Moffatt has apparently also said that Smith is officially the 13th regeneration of that particular Timelord. 11 Doctors + 1 War Doctor + 1 more for the time that Tennant regenerated into himself again, using his previously cut off hand as a blueprint or whatever. And since we know that Timelords are only supposed to get 13 regenerations, this may be a plot point in the Christmas special.