Was the bonus and repayment in the same year? If yes the employer must correct the W-2 taxable wages to reflect the repayment. If they won't or can't, yes, contact the IRS but the IRS says to wait until the end of February.
See this link from IRS for incorrect W-2
https://www.irs.gov/faqs/irs-procedures/w-2-additional-incorrect-lost-non-receipt-omitted
If repayment occurred in a subsequent year and was over $3000 different tax rules apply.
If this is your situation post back in this thread for what you should do.
