The TARDIS can certainly sense the tension in the atmosphere, but she still can't quite identify it. She's perfectly aware that Ianto harbors complicated feelings with regards to the Doctor, for reasons she doesn't entirely fault him for, but it irks her that he thinks this entitles him to judge her pilot on someone else's behalf. And that her word is apparently not good enough.

Nor does she appreciate that Ianto is apparently being fractious on purpose and trying to worry at the complicated matter of the Doctor's grandchild without possibly being able to understand. Her expression darkens, and she sets the fork down on the plate with a delicate clink before tightly folding her hands on the table. "The way it always does," she replies coolly. "She chose to stay in one place. We carried on travelling and he found new friends. Whatever else may change in him, his desire to care for those he loves does not." And if anyone can say that with any authority, it's certainly her.