I understand what Moffat is trying to do here. He's taking the "Can the companion/audience identification character adjust to the new Doctor and see through his new face to realize that he's the same person as before?" approach from "Robot" and "Castrovalva" and "The Christmas Invasion" and applying it with Capaldi's Doctor.
I don't think that works in this circumstance. Clara, more than any other companion, knows full well that the Doctor regenerates and has many faces. She's seen all of them and interacted personally with two previous Doctors. For her to suddenly go, two stories after the anniversary special, "Oooh, I don't know about this, this is weird and not right," doesn't make any sense for the character. She should really be -- and without the need of a phone call -- all like, "Oh, you've changed and I don't fancy you anymore, but you're still the Doctor, you're still my best friend, and let's see the universe." I'm not sure why Moffat thinks the characterization he's using for Clara works. Either he doesn't remember what he's written before, or he simply doesn't understand his own character. It's puzzling.
The more interesting approach for Moffat to take would have been, I think, to show us a Doctor who is 900 years out of practice, who knows it all but has to relearn the ropes, and is prone to making mistakes because he's rusty. But perhaps that's too much to ask; it would have meant that Moffat was able to grapple with the implications of his own stories, and he's not shown a great faculty with that.