To be fair, the one time she was perfectly hospitable for him, Peter didn't like her butterflies. This, however, is something on an entirely different level.

"What do you mean, it's you?" he asks, seriously confused. For all that he knows she's not in the least bit human, and for all that he's been told she is, in fact, a time machine, he still thinks of the TARDIS in terms of the woman he's looking at right now.