Yeah, how dare you presume incompetence on the part of Magic: The Gathering Online Exchange, the internet's largest online trading card site turned financial exchange. /s
(Not physical cards traded online, mind you, these were virtual cards in the game Magic: The Gathering Online.)
They were simultaneously bit by an attack exploiting a fault in their wallet implementation in combination with transaction malleability. You can invert all the bits in a transaction id and if you also take the complement of the signature then the signature is still valid. The transaction still happens but you never see the transaction ID come over the network (it's actually the complement of the txid). After a while, most clients concluded that it wasn't broadcast successfully and either aborted or retry, so their wallet balance diverged. And yes they probably did not check it against the official client balance.
A significant number of frontend nodes participated in this transaction malleability attack over a sustained period of time, probably more than a lone-wolf attacker could access (although renting botnets isn't all that expensive, especially if you are sucking out bitcoin at the same time...)
The interesting question is whether they had someone on the inside, although it could also be explained by incompetence and an attacker probing for weaknesses who comes to realize that the bug wasn't being patched.