A question asked not because the the person asking the question is actually wondering if someone is sitting "here", but more likely asked because the person wants to start a conversation with the person sitting next to the seat in question.
Dougy: "Is anybody sitting here?"
Girl sitting in class: "No..."
Dougy: "So whats up?"
Girl: *makes a strange look and moves away*
Dougy: "Dude whats her problem, she probably thought I was trying to hit on her or something...bahaha"