sometimes it catches them off guard. for example, if you're in class and you smile or look at them randomly without a real reason, it kind of freaks them out. sometimes they'll say it if they like you, too. depending on their tone of voice, of course. if they say it in a fake annoyed yet flirty kind of way, hmm...there's probably something there. but if they just snap at you, like "WHAT?!" then they're probably freaked out/actually annoyed by you.
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It could mean that he finds you attractive or interesting. It's a positive sign, and he may be trying to catch your attention or show that he is friendly.