Now Moffat has weighed in, throwing in an added (and odd) complexity regarding the Tenth Doctor's hand.
Anyway, it seems this will all be sorted out (or re-canonized) during the Christmas Special, Matt Smith's last outing as the Eleventh Doctor. Dramatically, no doubt.
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Steven Moffat has spoken about the Doctor's regeneration limit.
Speaking at the official Doctor Who 50th Celebration at ExCel London, Moffat said: "He has no more ever called himself the 11th Doctor than he would call himself Matt Smith. The Doctor doesn't know off the top of his head [what number he is].
"If you worry about such things, and I do, then I specifically said John Hurt's Doctor doesn't use the title. [Matt Smith's Doctor] is in his 12th body but he's the 11th Doctor, however there is no such character as the 11th Doctor – he's just The Doctor, that's what he calls himself.
"The numbering doesn't matter, except for those lists that you and I have been making for many years. So I've given you the option of not counting John Hurt numerically – he's the War Doctor."
When asked about the Doctor's regeneration limit, which was introduced in 1976 story 'The Deadly Assassin', starring Tom Baker, Moffat said:
"Paul McGann turns into John Hurt so they're not the same incarnation. He used up another regeneration and I expect he'll be in trouble shortly – you can't break rules laid down in 'The Deadly Assassin'"
Doctor Who returns on Christmas Day (25 December) on BBC One.
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He does call himself Eleven in The Lodger. The Minotaur's hotel also has his room as room 11, and there are a couple of other visual references to that number as well.
But then, pretty much everything that has ever come out of Moffat's mouth about what's going to happen on one of his shows is an outright lie, like how he swore that the Time Lords were absolutely and definitively dead and he had no interest in returning to Gallifrey.
To the point, +Brittany Constable, where it's unclear what's a lie and what's simply an abrupt and unexpected tack in another direction.