The current Doctor stated that taking the name "Doctor" is like a promise, and that the John Hurt character somehow broke that promise. The only question is, what did he do to break that promise? It was more than likely something involving the Time War (seeing as the only place we could have an extra Doctor is between McGann & Eccleston, during the war), but it could be anything really. If this were Davies, everything would relate back to the Time War, and this would probably be true, but this is Moffat. Moffat is likely to throw us a curveball, he could have done anything, really.
I'm really thinking that this promise is some sort of promise that all Time Lords and Ladies have to take, probably the promise not to interfere. We've already seen the Doctor interfere many times, and even get put on trial for it. He always managed to justify his interference by claiming to be saving innocent lives. Well, perhaps this regeneration killed innocents. He claimed to be doing it "in the name of peace and sanity," but the Matt Smith Doctor seems to think that it was a despicable act. He agrees with the motives, but claims it is something the Doctor would never do.
My wild guess: He predates William Hartnell; Hartnell was the First Doctor but Hurt wasn't the Doctor at all, so that would not affect the numbering. When the Pre-Doctor was born, his father was a powerful but prickish Time Lord (the only kind we ever seem to meet) who had forced his mother to live with him against her will. When their son was born she gave him a name that means "Pain" because her existence was so painful. Pain's father raises him as a chip off the old block, imbibing all that Time Lord arrogance. When he comes of age, Pain--played by John Hurt, which is what initially got me thinking about names synonymous with pain--has the chance to help somebody somewhere (let's say he has a chance to save the people of Mondas from the disaster that forced them to become Cybermen) but as a Time Lord he's sworn only to observe, never to interfere; so the terrible thing he does is done to preserve Gallifrey as an ivory tower. The guilt of this consumes him and he attempts to take his own life, then regenerates into William Hartnell. Feeling reborn he decides to renounce Gallifrey's corrupt ways and to symbolize this he will never again use the name that was given him, instead taking on a name associated with healing. That's the symbol of the promise he makes himself. He then tries to reform Gallifreyan society, but he's ostracized. The only allies he's able to pick up are people like the Master, the War Chief, and the Rani--who follow his example, renounce their given names, and choose new ones--but they're only helping him because repealing the doctrine of "only to observe, never to interfere" will allow their evil plans to flourish. His family disowns him, all but Susan, who believes in him and urges him to go into self-imposed exile.
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