It's not really confirmed whether mtgox funds were lost through some kind of malleability attack.
That's what they were claiming at some point, but they never showed any proofs, or even a technical explanation of how that would actually be possible.
The hypothesis regarding mtgox (fed by them, iirc) was that they were relying on transaction IDs to update their internal database of balances. So, there were withdrawals, then the attacker changed the transaction ID when they broadcast a transaction (the attacker was directly connected to them). So gox never decreased their balance since they were relying on the TX ID and they would withdraw again. (There were more details).
Again, poorly written non-bitcoin network software IF that is what happened.