Yes, you are correct, if that's what actually happened. Do you have your paystubs from this company? Federal Income Tax withholding comes from your pay. It doesn't come from any employer contributions. If he reported too much withholding, he'd have to amend his 941s to show that. And yes, you would be paying the IRS back your refund if the withholding was wrong on your W-2. Don't pay the employer.
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