I suspect it's all of these, in no particular order:

- lost coins through hacks, maybe years ago
- FBI seizings
- malfunctioning MtGox code
- mismanaged cold wallets
- fractional reserve speculating


All these contributed to the sorry state they are in now. Maybe they sold coins to fund their liquidity problems in August, only to see the price of bitcoin skyrocket, catching them with their pants down. Maybe they misplaced some vital private keys. Who knows?

All I know is that they didn't lose 800k in bitcoins through transaction malleability and nothing else. That's bullshit.