And both Madame Vastra and the new Doctor kind of hint that there was a romantic dimension to the relationship between Clara and the Matt Smith Doctor, which can't continue now that the Doctor looks like Peter Capaldi. Flirting with the Doctor is like flirting with a mountain, Madame Vastra explains, but in fact the Doctor's formerly cute visage was his way of flirting with Clara, and others like her.
(And meanwhile, the Doctor keeps almost flirting with the female dinosaur, and finally actually says, "I'm not flirting.")
The relationship between the new Doctor and Clara, though, is set up as being somewhat dysfunctional. All of their conversations seem to consist of him accusing her of being a needy egomaniac who plays games. Or a control freak — which, accusing someone of being a control freak is basically a way of manipulating them into giving up control.
Just when you think that this new Doctor is going to be too horrible for Clara to deal with, he reveals his deep inner pain, and says that it was he, not she, who thought that he was her boyfriend. The Doctor was flirting with her by using a young, dashing face, and seeing her as a romantic prospect - but that's all over now.
And then Clara gets a very moving phone call from the dying Matt Smith Doctor, sent through time to his own future. The Eleventh Doctor tells her that the Twelfth Doctor is more scared than she is, and she needs to help him. And the Twelfth Doctor emerges from the TARDIS and accuses her of not seeing him — a callback to Madame Vastra's thing of saying the Doctor's face is his veil, through which you can't see the "real" him. The Twelfth Doctor gives her some puppy-dog eyes, and she hugs him.
The whole thing feels just slightly weird, to be honest. The Doctor keeps undermining her — even when she's been utterly awesome, he says that she triumphed over the robots because she was "5'1 and crying." But when she's finally had enough of his meanness, he shows his wounded side and makes her feel sorry for him.