A prepayment was made in October but the invoice was not issued until November. How do you correct this?

Re issue the invoice as a credit. The account should have shown a credit balance to begin with. If an invoice has been sent out in November showing a balance owing, forward the clients credit to apply to the invoice, and send the corrected invoice to the client for your reference. Then make note on the original November invoice of the number of the invoice with the correction. Best to explain mistakes than try to hide them.