how to correct wrong clin paid by contracting officer and apply funds to correct clin

You need to follow any specific instructions that your contracting officer gives you.

Hopefully, the Government will correct its error on its own books and leave you out of it.  Or, maybe you will have to submit revised invoices.

Let me add.   Do not forget to consult the specific of your contract as well.  By example if your contract is a Commercial Item Contract and FAR Clause 52.212-4 is in the contract as it is found in the FAR, in other words not tailored, you may have some responsibility as well as the erroneous payment language of paragraph (i)(5) of the clause.....

" (5) Overpayments. If the Contractor becomes aware of a duplicate contract financing or invoice payment or that the Government has otherwise overpaid on a contract financing or invoice payment, the Contractor shall-...."