My understanding of the problem is that some people went to withdraw money and due to transaction malleability MtGox thought the transaction failed and resent repeatedly. But the first transaction didn't actually fail and they received their money multiple times.
Whether this happened to a lot of people a little or a few people a lot, and whether they were accidental beneficiaries or intentional instigators will probably never be known. But some number of people received a share of that missing 750k BTC, and I don't recall a one of them posting a "Hey, MtGox just sent me more BTC than it should have" blogpost that ended up here, so that's pretty interesting.
So the BTC aren't missing so much as illicitly redistributed.
In a lot of software engineering, Good Enough really is good enough. But a 5 cent discrepancy between what you actually have and what you thought you had need to be treated as seriously as a $5 million discrepancy.