Manually create Credit note

Hi there,
From reading your documentation – the only way to issue a credit note on an invoice is when the order is marked as refunded. However, in some cases such as paying by Credit Card, the order can cancel if it exceeds the timelimit. It still generates an invoice though. Is there a way to disable this & only allow the creation of invoices on a “Completed” order? Also, how would we create a credit note for the “cancelled” orders?

Many many thanks!