Most likely, they screwed up and lost their private keys. ie: Plain old incompetence.
The code that was leaked to pastebin made it look like they were storing these in something like instances on Amazon EC2. If it turned out they were storing it on ephemeral storage rather than EBS, I don't know if I'd laugh or cry. But it would be an explanation if it were true. Again tough, that would come back to incompetence.