If you entered the W-2s properly the program should automatically do all the calculation and adjustment.

IRS even came up with a couple of forms to take care of this. Look closely at the return to see if you can follow the flow 

The program knows the refund is due. When I force the 8959, the credit appears on the 1040 - then error check tells me my client doesn't qualify and I will have to paper file. The excess SS does not appear on the Schedule 1, line 11 and I know I entered it correctly. There was some initial confusion when payroll was set up - single owner Sub S and some benefits are taxable and some are not. I don't want to hold up the refund for a few hundred dollars and mailing in is, in my opinion, not a good option. I'm still working on paper that was sent in over a year ago, I don't want to start another thread. At this point all I can see is to file and let the SSA figure out there's an overpayment and send a check.

If this is an employer error, the employer has to fix it and refund the erroneous SS tax.  The mechanism built in to the 1040 (2021 Schedule 3 Line 11) is if there are multiple employers and the total withheld exceeds the maximum.