No. If you are overpaying your taxes, this will not cause you any trouble, other than you will need to file a return to claim a refund of the taxes that you paid that you didn't need to pay. You do not get in trouble for getting a refund, but you can get penalties if you do not have enough withheld throughout the year.
If you do not otherwise file a return, you would need to in order to claim a refund of taxes paid. If this is the case, you can also ask your boss why he is withholding taxes when they do not need to be withheld as your income is below the standard deduction.
Be aware though, if you do go over the standard deduction at all, say you get another job or a raise, then you could have taxable income and then having a small amount withheld throughout the year could help you to cover any tax liability you may have so you do not owe as much or you may still end up getting a refund.
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