prepare and file your return. if there is no underpayment penalty you don't have much to complain about. you owe but had the use of the money for a substantial period of time. if there is you can include a letter, signed and dated, with your return which would have to be mailed asking for abatement of the penalty because it was your employer who failed to properly withhold even though it had on file a properly completed form w-4. You could also e-file and await the penalty notice and then return the notice with the same letter. abatement is up to the IRS. if the IRS abates the penalty all well and good. if not ask your employer to reimburse you and if they will be including the amount on your next w-2 wages they should increase it because you'll pay taxes on it
