@NCperson Medicare tax withholding is not "simply 1.45% of Box 5." Each employer must also withhold 0.9% Additional Medicare Tax on Medicare wages over $200,000. The total Additional Medicare Tax withheld is calculated in Part V of Form 8959 and credited as additional withholding on Form 1040 line 25c. It's that additional withholding from Form 8959 that the IRS disallowed. But it's not clear that there was any overwithholding. The disallowance might be an IRS mistake. The OP, billschwamle, has apparently purchased Audit Defense, so hopefully they will straighten it out.
