You have to look at your pay stubs to see if the tax had actually been withheld. If so, your employer should reimburse you for the federal tax withheld. If the IRS processes your return as you filed it, with the tax reported as withheld, then you will need to file an amended return to reflect the corrected W-2 form. Also, if you don't file the amended return the IRS will send you a letter eventually requesting the missing tax that may include penalties and interest.
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