This is the third episode in a row that the Doctor "doesn't know" who or what is going on. He didn't know who is behind the mummy train, who the inter-dimensional beings are, and initially, why the forest suddenly appeared. He even said to Clara that people will forget the forest, like they forgot the last crisis (Battle Of Canary Wharf?).
Even in the trailer for next week, he doesn't seem to recognise Missy, although this maybe for trailer/spoiler purposes.
Maybe this is an in-joke on Capaldi's age/this Doctor's grumpiness, or maybe a re-boot?