Those are what you call closet sexists. They want you to feel bad about being a girl, but dont want to be overt about it. So they poke at you with stupid comment like that probably thinking theyre being clever by being inconspicuous, but like aryman said are probably just jealous jerks who will use the fact that youre a girl to trick themselves and try to trick you into thinking you recieved some sort of affirmitive action so they dont have to feel bad about being "inferior". Don't let them do it! Have some confidence in yourself!
Unfortunately thats not the first time you'll meet people like that. Closet sexists or racists. They do whatever they can to avoid the actual label of course