"The Creature from the Pit," I believe. Not the first time ever but it was, IIRC, the first time on the new series. There had been a few instances on the classic series where numbers had been mentioned. Richard Hurndall referred to himself as "the original" in "The Five Doctors." The Time Lords also referred to Hartnell as the 1st Doctor in "The Three Doctors." (So we really need to reexamine how we interpret "The Brain of Morbius." Not really a problem since it's pretty vague on how the mind-duel works anyway.) RTD kept the time period between the Paul McGann movie & Eccleston's debut extremely vague and there could have been all kinds of new Doctors in there that we never knew about, or not. RTD didn't really pin things down too hard at all until we saw the little flashback recap of the previous Doctors in "The Next Doctor." Moffat was a lot more blatant, first by calling Smith's first episode "The Eleventh Hour," and then even more so when the Doctor referred to himself as "eleventh" in "The Lodger." Then we get the "Fall of the Eleventh" references in "The Wedding of River Song." I can't really recall that many instances of things that are "contrary" to the existence of the NX-01. They got around a lot of the natural problems with it by having it be the Enterprise from the pre-Federation version of Starfleet, so it doesn't count for numbering purposes. The only instance I can think of where it would really have been natural to refer to the NX-01 and they didn't was when we saw all of the previous Enterprises on the rec deck in Star Trek: The Motion Picture. Speaking of Star Trek, this whole thing with the John Hurt Doctor is reminding me of that DS9 episode where we found out that there was another Dax host between Torias & Curzon who's existence had previously been hidden because he was a murderer.