I use S3 for hosting static sites only, and only in North American zones.
Some time ago, I see some billing lines stating:
"US West (Oregon) data transfer to Asia Pacific (Tokyo) 0.001 GB $0.01"
I had no idea why I'd be paying for transfer to a zone outside my own. Obviously I don't care about the 1cent, but my small problem may be someone else's big problem.
Instead of looking into it, they refunded me a month of service (a few dollars).
I guess that's the opposite of @QuinnPig's thought, but seriously, what was the charge for? Someone running their own crawler on EC2 so I paid for internal DC-DC charges?