Even when one believed they were being completely discreet, there is a feeling that is difficult to mask when someone stares for any length of time at another person. Perhaps it was because of her years as a Death Eater that Hermione could identify the impression of eyes boring into her while she appeared to be sleeping. Maybe all of her training with Antonin prepared her for what it would be like. She wasn't sure. It didn't matter. More than a few times being able to pick up on that prickly sensation saved her life when others around her meant her harm.