If you adjusted the Bitcoin amount of a payment manually and you made a mistake in the process, you can always recover this transaction through BitPay. They process and manage the Bitcoin payments for us.
If you did not pay enough, the BitPay payment page will display the following message (after a 15-minute waiting period): "This invoice has expired before it was fully paid". Right below it you will see a button 'Request refund'. A request will be sent to BitPay by email; they will handle the refund of your Bitcoins from there.
If you paid too much you can also ask for a refund from BitPay through the same procedure.