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.
Are they still a functioning company? If they are, I'd be amazed to see them around much longer, this is BAD press, and makes the company leaders look pretty incompetent