I contacted support via Apple Developer page > support > contact us. They refunded the extra charge. Took about 6 hours for the reply. It will take the usual upto ~15 days for banks to process it, but I got the email with the refund invoice/credit pdf.

I contacted support via Apple Developer page > Support > contact us. And they refunded the web payment, took ~6 hours for the confirmation. (up to 15 days for refund to appear in bank, but I got the invoice with negative amount.)