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In season 9, episode 4 (or story 2 part 2) Before The Flood, The Doctor tells Clara that he is going to die.

CLARA: No. You can change things.

DOCTOR: I can't. Even the tiniest change, the ramifications could be catastrophic. It could spread carnage and chaos across the universe like ripples on a pond. Oh, well, I've had a good innings. (to O'Donnell) This regeneration, it's a bit of a clerical error anyway. (to Clara) I've got to go sometime.

Season 9 Episode 4: Before the Flood. Transcript from Chakoteya.net.

What does the Doctor mean when he says "It's a clerical error" in regards to regeneration.

Aster
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After he hears his ghost has appeared, the following discussion happens:

Doctor: It means I die.

Clara: No - not necessarily. We can change the sequence of events so...

Doctor: This isn't a potential future, this is the future now. It's already happened. The proof is right there in front of you. I have to die.

Clara: No. You can change things.

Doctor: I can't. Even the tiniest change, the ramifications could be catastrophic. It could spread carnage and chaos across the universe like ripples on a pond. Ah, well, I've had a good innings. This regeneration is a bit of a clerical error anyway.

This is a reference to all the hoopla about which generation he's on.

BCdotWEB
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  • Ah! I misheard it as referring to regeneration in general. Welp. – Aster Oct 10 '15 at 20:59
  • Wow, I feel kinda stupid for forgetting the whole "he ran out of regenerations already" thing. +1 – Ixrec Oct 10 '15 at 21:00
  • Isn't this the first of a new regeneration cycle though? Am I falsely remembering that the Time-Lords sent him a new regeneration cycle in (I think) Time of the Doctor? – ZenLogic Oct 10 '15 at 21:40
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    They did... And it's unsure how much regeneration energy he spent in the previous episode as well... We don't know how many regenerations he has left in general. – DoctorWho22 Oct 11 '15 at 02:18
  • @DoctorWho22 Yeah, not to mention all the regeneration energy he spent in defeating the Daleks (also in Time of the Doctor). – Mr Lister Oct 11 '15 at 09:39
  • That too but who knows if that was actually just spill off from gaining the new cycle or whether or not he actually spent regeneration energy used for future stuff. Recall how sometimes when The Doctor regenerates the energy spews out and sometimes damages stuff around him. Like how the 10th into 11th regeneration caused a lot of damage to The Tardis. – DoctorWho22 Oct 11 '15 at 14:59
  • I figured he meant he wasn't supposed to get more regenerations after the 12th, hence the "clerical" error. Even Eleven said it: "Regeneration number 13!! We're breaking some serious science here, boys!!" – tilley31 Oct 12 '15 at 16:29
  • @DoctorWho22 I vaguely remember The Doctor saying something like "I'll probably lose an arm or a leg or something somewhere down the line", in S9E2 -- so I'd imagine that it's the latter.

    Let us not forget rule one though ;)

    – Aster Oct 12 '15 at 22:17
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You know what? After watching the episode for the third time I'm turning my comment into an answer. I really think he means his current regeneration wasn't supposed to happen to begin with.

Back in "The Time of The Doctor", after Eleven got the new cycle from the Time Lords and starter regenerating, he said this (emphasis mine):

[A crack in time opens in the sky, and regeneration energy drifts down from the crack into the Doctor's mouth.]

Dalek Commander: You will die now, Doctor. This is the end of you! The rules of regeneration are known. You have expended all your lives!

The Doctor: Sorry, what did you say? Did you mention the rules? Now, listen. A bit of advice: tell me the truth if you think you know it, lay down the law if you're feeling brave, but, Daleks, never ever tell me the rules!

Dalek Commander: Emergency! Emergency! The Doctor is regenerating! The Doctor is regenerating!

[The clock tower begins to strike twelve]

The Doctor: Oh, look at this! Regeneration number thirteen! We're breaking some serious science here, boys! And I tell you what, it's gonna be a whopper!

The clerical error means that a Time Lord can't regenerate for a 13th time, at least not naturally.

tilley31
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It's just Steven Moffat and his bruised ego. There was an initial fan backlash against the choice of actor, so Moffat is just putting sarcastic jabs at the audience in there — it's not the first time he's done that. Notice how the Doctor breaks the fourth wall as he is saying it? It's Moffat flipping the bird to people who criticize him, that's all.

FuzzyBoots
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  • Welcome to SFF.SE! Can you provide any evidence, maybe in form of an interview or similar, to support this claim? – Skooba Sep 23 '17 at 12:51