The amount does not matter, it is still considered false accounting/fraud.
You said you can only refund it if they complain, please send a newsletter to ALL of your customers asking them to check their account and ask for a refund if there are discrepencies.
+1
I don't have a dog in this fight, but it sure as hell stinks like scrypt.cc's 'autobuy' shenanigans recently and they are a proven and confirmed ponzi. For your firm to not immediately send out notices to customers advising them to check the status of their account due to this error is unprofessional, to say the least.
It would almost seem like you were counting on the fact that a whole bunch of customers wouldn't notice.