I am having the same issue.  S Corp with employee retention credit.  I entered the credit on the Schedule M-1/Reconciliation of Income Deduction Items line 2.  The amount flowed to the k-1 line 13 with code P.

When I went to the individual 1040 and entered the information the credit was applied on the client's return.  The result was a fairly substantial refund for this client.  Anyway, I knew that couldn't be correct.  As is mentioned on this thread the credit is a payroll credit.  I understand the wage expense should be reduced for the credit amount.  It sounds as though the credit is not separately identified on the 1120S or the 1040 at all, otherwise there is a "double dipping" result of the credit on the 1040.  The result is the W3 total wages will not agree to the amount on the 

To add to confusion, the title of form 5884-A is Employee Retention Credit.  Jeeze, couldn't they at least call it something else!