Annabeth didn't like Jason.
When Jason came, everyone looked up to him. He was a child of Zeus, the first since Thalia.
When Jason came back from his quest, everyone admired him. Percy faded into the background, became 'that one who saved Olympus once.'
Jason became a hero, but he wasn't truly. Percy was the hero of Olympus, but everyone forgot. And along with Percy, they forgot Annabeth's pain. They pressured her to get better, not knowing what she was feeling. They didn't get it.
Annabeth knew better. Jason was a replacement, that was all. Percy was the true hero.