One obvious hole I can see in Facebook's story is that they insinuate that Wes broke back into the server after they disputed the bounty. If this were true, they did nothing in response to the problems Wes found for over a month.
If you look at Wes's timeline, he says access to the server was no longer possible a few days after he filed the second report.
It comes down to who you believe. Personally, I find Wes to be more credible. It sounds like it was most likely a misunderstanding by FaceBook. Now they are doing damage control.