at that point, she was denying that she loved him. She was not willing to believe that she was in love, and that Neo was the One they had been searching for. It wasn't until Neo had a magazine emptied into him that she accepted her love for him, and part of this is why Neo came back. Neo had to die, and Trinity had to accept her love for him, for Neo to become the One. It was like the Oracle said. He had the potential, but he was waiting on something.