If you haven't already done so by the time you read this response get in touch with your disgruntled buyer via eBay Messages, explaining that the additional postage was due to an eBay glitch and that you will refund the extra money, making sure that once you've sent the message you actually do refund the buyer the extra postage costs that he/she shouldn't have had to pay. At least that way if the buyer hasn't already left you feedback then he/she may be less likely to mark you down on the postage costs and/or leave you a negative feedback comment, as the problem that resulted in the complaint would have been resolved, and the buyer wouldn't be able to justifiably say "I got screwed over on the postage costs by that seller..."
In the event that the buyer has already left you negative feedback by the time you read this reply refund the extra postage anyway, then send the buyer a Feedback Revision Request. If the buyer can see that you are genuinely trying to help to resolve the problem, and ends up believing your explanation that it was caused by an eBay glitch, then he/she may be willing to revise any negative feedback left.
