It's not that she doesn't notice. It's more that she doesn't understand it. "Complicated? If it's not intimate and it's not everything the Master said then why is it complicated?"

And then another thought occurs to her. "What else did she see, Doctor? Why does she look at me the way you do?" Now there's panic in her voice. There are things in the Doctor's head that she would never want anyone to see. "What does she know about you and me?"