As explained in the ending, it was all very simple: The Time Lord known as The Doctor has had 12 bodies, 11 of them were known as 'The Doctor' save one, the one played by John Hurt. The reason why the John Hurt Doctor isn't called 'The Doctor' is because he did something so horrible, he could in no way ever be considered 'The Doctor', the word for healer or wise man. This means that while this makes Eccleston the 10th incarnation, Tennant the 11th incarnation, and Smith the 12th incarnation, they still remain as the 9th, 10th, and 11th Doctors respectively.
Now, the John Hurt Doctor was likely the Doctor between Doctors 8 and 9, meaning that the horrible thing he done? Was most likely during the Time War.
Think about it. What is the one regeneration we didn't see? McGann to Eccleston.