By not disclosing this earlier I also wonder what else the company could be hiding. I've just lost a lot of faith in Bitpay. As for this happening in legacy bank systems - they could probably just reverse the mistaked transaction. Fungibility is not such a big deal for them.
Wire fraud is still a huge problem for the traditional banking system. Sometimes they can be reversed but generally once the fraud is detected it is too late for the money to be retrieved.