Since I don't anticipate getting a chance to point it out inside the fic itself, and the hint is unreasonably subtle:

When Hermione woke the third time (though it felt like she'd only closed her eyes for a moment) the Sun was even lower in the sky, almost fully set. She felt a little more alive and, strangely, even more exhausted. This time it was Professor Flitwick who was standing next to her bed and shaking her shoulder, a tray of steaming food floating next to him. For some reason she'd thought Harry Potter ought to be leaning over her bedside, but he wasn't there. Had she dreamed that? She couldn't remember dreaming.

Harry didn't think of it instantly, but given a little time...