Excess Social Security tax withheld not add back to Federal refund

If you have more than one W-2 with the same EIN, but one of the W-2s is for the employer acting as an agent for the other employer, the program unfortunately does not pick this up properly.  You need to fix it by using the 1040 worksheet and entering it in Part II on the smart worksheet for this purpose.  In this instance, you do NOT go back to the employer but rather claim it as a credit on the tax return.

If e-filing, make sure the names are entered properly on the W-2 worksheets indicating that an agent situation exists and attach as a pdf the relevant instructions from Form W-2 and the Internal Revenue Manual.  Chances are though you will still get a notice.  Alternatively, you could file on paper, with above documentation attached and with an explanation on Form 8948 that the reason you are filing on paper is in the hope a human will read this and the attachments and head off the inevitable notice you will get if efiling.

When I have encountered this and efiled, a notice came.  When I paper filed, knock on wood, there has never been a notice so maybe they actually do read and look at it.

If this isn't your case, a little more info would be helpful.