The Doctor has rarely cared about clearance or anyone's permissions where his TARDIS is concerned. But he doesn't want too much conflict, so he whips out his psychic paper and flashes it at her as he speaks. "Well, here's the paperwork, all in order. Just here to check on my TARDIS."

And just as quickly the psychic paper goes away. And he continues to approach the TARDIS. As he gets closer, he talks to himself. "No, no, no! This is all wrong. She's too young. Oh, what have they done?"

It's his TARDIS, of that he has no doubt, but she's from another time. That's very not good. But he needs to get closer to make sure.