As far as your tax return goes the answer is the same as above - you have to fill out your taxes and take the hit. The taxes that you are paying at the end of the year are the same that you would have paid if the withholding had been done correctly, just now all at once. The IRS expects to get paid one way or another.
As far as what to do about your employer you can report them to the IRS for failing to withhold correctly. Especially if you can document your back and forth with them about the correct amount you requested be deducted. If they are doing it to you they may very well be doing it to other employees. Here is where to report an employer.
In addition, you may have reason to report your employer to the authorities in your state. You'll have to check the laws in your state about that.
@TheWhiteMocha
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