Maius Intra Qua Extra

Oh, it's not even a matter of continuity. Moffat decided that he wanted Clara to be responsible for everything the Doctor is and did. Through her tenure she

• was responsible for every victory the Doctor ever accomplished ("The Time of the Doctor" - the one you saw),
  
• appeared to the Doctor as a young boy and inspired him to travel the stars ("Listen"),
  
• directed the Doctor to choose the TARDIS ("The Time of the Doctor", in direct contradiction to "The Doctor's Wife"), and
  
• was the person prophecied by the Time Lords to be destined to destroy Gallifrey, which was why the Doctor originally left Gallifrey, to escape his role in the prophecy.
  

Basically, Moffat rewrote the entire history of the show so that she (and by extension, himself) is responsible for all of it. And, in "Heaven Sent" (which is honestly a fantastic episode despite what I'm going to say), which occurs after Clara left, we get to see his thought processes, and he was incapable of acting at all without talking to an internal vision of Clara, who told him what to do.

This is why I don't write fanfic for anything past Amy and Rory. I just ignore the destruction that Moffat wreaked on the show and pretend it never happened.