Can I get in trouble for selling fake Sony PS3 controllers on ebay?

Going to the authorities yourself would have been the best ideas. That shows you did not intently distribute these fake controller. You have destroyed what sound like a big part of your defense, giving a refund was in your best intereste but it still does not eliminate the others that are out there and that you are probably not the only one. This needs to be reported not only to the authorities but the Better Business Bureau so that others wont get scammed.