Your job didn't take out the actual tax. The federal tax withheld in box 2 is just an estimate to apply to the total tax on all your income. The tax withholding wasn't enough to cover the actual tax on your return. You can give your employer a new W4 to gave more taxes taken out for next year. Oh and you only get back from W2 box 2 and 17 for state. Not boxes 4&6. Those are mandatory taxes.
