DISCLAIMER: I'm not confirming that this is what Moffat believes or is referring to. It is merely my opinion regarding what I think he's referring to. I know a lot of folks out there have some pretty passionate opinions about The Doctor's regenerations (Morbius lunatics I'm looking at you), and what I've depicted here is merely my personal contribution to the larger debate. It makes sense to me, especially from what I suspect would be the point of view of the series' writers, and what Moffat (an uber fan of the original series) would use to justify that only 11 regenerations will have taken place as of Capaldi's Doctor according to the canon depicted on the show. Rewatch your DVDs of The War Games if you don't believe me.
[EDIT/UPDATE 12/17/13]: Steven Moffat has come out in an interview recently to state that from his point of view (which is basically what my speculation is meant to address) that all of the Doctor's regenerations have indeed been used up, by reaffirming the change of appearance as an actual regeneration and that the meta-crises also counts. His stated intention is that the Christmas episode will directly address how the 11th Doctor will become the 12th without breaking the rule about regenerating only twelve times. Personally I thought he was going to address the regeneration limit at the end of a future regeneration, but it seems that the 2013 Christmas special will be when the question we've all been asking ourselves since we first realized the Doctor was nearing the end of cycle will be answered. I'll update the description to this post again after the Christmas special to reaffirm what we learn (though I'll probably wait a few days to avoid spoilers for folks that don't get to see it right away). For the time being I'll leave the image above unaltered to preserve as an homage to the bit of fan speculation that I partook in when trying to scrute the inscrutable mind of Moffat.