Why were there 13 Doctors prior to #12?

Thirteen Doctors encapsulated Gallifrey in The Day of the Doctor. But in The Time of the Doctor it mentioned 13 prior to his regeneration at the end of the episode. I count 12: #11 plus the War Doctor.

Where is the 13th Doctor?

Answer

The thirteen Doctors/TARDISes in Day of the Doctor don't map to the twelve regenerations that Eleven counts out in Time of the Doctor.

The Twelfth Doctor makes an appearance in The Day of the Doctor.

Peter Capaldi's eyebrows have a cameo ("No, sir: all thirteen!") in The Day of the Doctor.

Exhibit A: Capaldi's eyebrows

So we get to see the First, Second, Third, Fourth, Fifth, Sixth, Seventh, Eighth, Warth, Ninth, Tenth, Eleventh, and Twelfth Doctors whizzing about in their TARDISes.

But The Time of the Doctor isn't counting Doctors; it's counting regenerations.

The Tenth Doctor was forced to regenerate in The Stolen Earth and Journey's End, but he used a trick to create the Meta-Crisis Doctor and keep his own face ("I had vanity issues").

Ten cheats.

This counts as a regeneration (but not a new Doctor) because it used up one of the packets of bio-energy Time Lords use to power their regenerations. The Meta-Crisis Doctor is largely human, doesn't have his own TARDIS to buzz around in (deleted scene debates notwithstanding), and is stuck in an alternate universe, so he doesn't count and didn't get invited to the saving-Gallifrey party.

Capaldi's Doctor doesn't get included in this regeneration count because at the time he hadn't happened yet.

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