Disclaimer- I don't own Harry Potter.
Hermione didn't notice when she had stopped noticing Harry.
She didn't notice when the times came that she would have sworn he was in the boy's dorms, but seen him walk in from the halls, or how many times she could have sworn he was at Quidditch practice, when he was in detention. Or the other way around.
Hermione didn't like being faced with her own ignorance. She normally avoided that by all the books she reads. That's why she decided it was time to figure out Harry again.
What are his main characteristics? Does he still dream of Voldemort? Does he still understand all the work enough that he doesn't need me? Does he know what he wants to do after he graduates?
Hermione felt that these answers that she was missing, were important. And she didn't have them.
She started watching Harry more. She quickly noticed that Harry always used the word Fine, when he was asked how he was. Always. Never good, never great, or anything else. Always fine.
She noticed most of the time, he was either Happy, Mad, or in pain. She thought that the last was because of detention with Umbridge, or Voldemort, who now had a stronger connection. Harry never got hit with a bludger, no matter how close it got. He didn't plan anything past Hogwarts because he didn't expect to live that long.
Harry had a good poker face if he needed it, though he'd run a hand through his hair when angry.
Harry had changed when she wasn't looking. What else was she missing?