But if Medicare Wages are only $86,099 then there would be no Additional Medicare Taxes withheld.  Additional Medicare Taxes only get withheld on wages in excess of $200,000.  Does this situation include a predecessor/successor employer?  That's the only reason I can think of that there would be Additional Medicare Taxes withheld for wages < $200K.

Prior to ACA, having too much (regular) Medicare tax withheld would be an employer problem and the employee's recourse would be to go back to the employer and request a refund.  ProSeries used to throw off a diagnostic message warning the preparer to check the medicare/social security amounts entered on the W-2 Wks.  I'm not sure if it still does.

It sounds like your problem is that the employer withheld too much regular Medicare tax, not that the employer withheld Additional Medicare Tax.  Maybe now because of the convoluted approach the IRS takes to handling Additional Medicare Taxes these concepts are interchangeable but I won't believe that until I see a client with a refund from the IRS!

In your case, did the IRS send a $681 check?  This stuff will usually get caught on the employer side if/when the quarterly 941 totals don't agree with the W-3 totals.

Rick