Prevent Duplicate Payments

You can use the following snippet:

add_action( 'admin_enqueue_scripts', function ( $hook ) {
    if ( $hook === 'woocommerce_page_wc-orders' ) {
        ?>
        <script>
            function confirmManualPayment( event ) {
                event.preventDefault();

                if (
                    ( event.type === 'keypress' && event.keyCode === 13 && event.target?.matches( '#charge *' ) ) ||
                    ( event.type === 'click' && event.target?.id === 'charge-btn' )
                ) {
                    if ( jQuery( '#_transaction_id' ).val() ) {
                        if ( ! confirm( 'There is already a payment on this order. Would you like to proceed?' ) ) {
                            event.stopPropagation();
                        }
                    }
                }
            }

            document.addEventListener( 'keypress', confirmManualPayment, true );
            document.addEventListener( 'click', confirmManualPayment, true );
        </script>
        <?php
    }
} );

This will only work if the customer paid using a payment method that fills out the WooCommerce Transaction ID field (which you can see when editing Billing fields on the order screen). It determines whether a payment has been made by checking if that field is filled out. If you use other payment methods that don’t use that field, you’ll need to determine whether the order has been paid by some other check. Gateways like Stripe use that field.

Also, this snippet depends on some internal implementation details of WooCommerce and Woo MP, so it may need to be updated if either plugin changes something relevant.

That snippet does not cover that scenario. It would be more complicated to cover that.