I am guessing that you haven't received the funds for this sale which is now cancelled but you had funds available awaiting payment from a previous sale.
The funds for the cancelled sale are on hold not yet processed to your available funds so the refund comes from your available funds and your payment source to make up the difference - once the refund goes through ebay will release the held funds to your available funds usually on the next day.
I know it seems unfair but it is a timing issue between funds going to ebay then to you then to the customer who cancelled