Yea, what's the fucking story here? I thought that all BTC transactions are recorded and permanently stored as part of the "block chain". So let's look at the transaction history; where did all the coins go? This was a heist greater than any bank robbery in history - Where is the FBI?
This is a very interesting problem, and the answer is quite complicated. This is what I have been able to gather from public sources, held together with various deductions and educated guesses.
1. Mt Gox is an exchange. You can deposit or withdraw legal currency and trade for BTC or vice versa.
2. There is by necessity a pool of BTC and legal tender held at Mt Gox in place of client funds. In the case of BTC, a customer would pay BTC from their wallet to Mt Gox's wallet address, and the opposite would happen for withdrawal.
3. While BTC payments are public via the blockchain, the exchange of legal tender for BTC is not a blockchain transaction and therefore not public and only logged internally in Mt Gox's database (although summary information - e.g. trade price and volume - is published).
4. The deposit of BTC into Mt Gox and withdrawral out are part of the blockchain and are publicly logged.
5. Mt Gox wrote custom "wallet" software to handle the BTC transactions on the blockchain. It had a serious bug, in that the payment instructions it generated were malformed.
6. The malformed transactions would be accepted by early versions of the official bitcoin client, and the transactions would work correctly. However, the hash of the transaction data (often used as a "unique ID") would be different in a malformed transaction compared to a correctly formed one.
7. The bitcoin developers realised that this would be a problem, and pushed out an update that would automatically reject malformed transactions, even if otherwise correct and signed. They also sent out an alert to developers telling them that the transaction hash must NOT be used for tracking the progress of transactions (because if two copies of the same transaction, one well formed, one malformed had different hashes, and you only look for one hash, then you may think the transaction had failed, when it had in fact, completed).
8. Mt Gox failed to implement this when the update was pushed out in Jan 2013. As a result, BTC withdrawals from MtGox would fail. MtGox internal developers were unable to identify the problem.
9. 3rd parties unknown (possibly hackers, possibly frustrated customers of Gox trying to withdraw BTC, possibly benevolent 3rd party bitcoin proponents) set up "workaround" servers. These would pick up the malformed transactions from Mt Gox when they were broadcast, and they would reformat them into the correct format required by the blockchain and then rebroadcast them. The blockchain would ignore the malformed broadcasts, but accept the reformmated broadcasts.
10. Not only had Mt Gox not noticed the bitcoin protocol update, but they had also not heeded the warning of the bitcoin devs to be certain that they are not using transaction hashes for checking transaction progress.
11. The Mt Gox wallet software used the transaction hashes as the ONLY method of reconciling transactions. The blockchain was never rescanned to check that coins were in their expected places, and the coins were never traced as part of transaction validation. (This contrasts with the reference source code, which reconciles transactions by tracing the coins as they progress through the blockchain).
12. Over the next 12 months, confusion reigned at Mt Gox and they had no idea why sometimes customers would complain about not receiving transactions, and that they could not find the transaction hashes in the blockchain.
13. To Mt Gox's wallet software the transaction might appear to have failed (because the hash would never appear in the blockchain due to the transaciton being malformed). The same would be true for Mt Gox support, who would search for the transaction hash on blockchain.info and not find it. As a result, support would reissue the transaction without any further checks (e.g. checking the receiving address on blockchain.info for receipt of coins, or checking the MtGox wallet address for withdrawal of coins)
14. There appears to have been mass exploitation of this lack of checks. Some customers are believed to have noticed that they received their withdrawals, but that the transaction was showing as failed on Mt Gox, and that they had the "wrong" transaction hash listed. Some customers may then have gone and received double or triple payouts from support by claiming that the coins never arrived.
15. It appears that there was no auditing of this over the 12 month period when all withdrawals would have been subject to this bug (and possible several years previously, as the hash "malleability" bug was first noted in 2011, and the developers started warning software devs about it)
16. Mt Gox held a limited size "hot" wallet for day-to-day BTC use. The vast bulk of their BTC were held in a stack of "cold" wallets that would hold their long-term customer deposits in an offline/nearline format.
17. On Feb 7 2014, Mt Gox were finding that no more BTC withdrawrals could be made. From what i can tell, this is because their "hot" wallet was empty. The status of the "cold" wallets is unknown, but they are rumored to be depleted also.
18. It is presumed that they had either an automated system or a manual process with no checking for transferring BTC from "cold" to "hot". This appears never to have been audited or subjected to checking.
19. New MtGox customers would have had to supply scans of passport/photo ID/proof of address/residency. However, it is possible that old customer accounts might not have needed this, especially if they never tried to deposit or withdraw legal tender (i.e. only move BTC in and out for speculation purposes).
20. While it should be possible to trace customers that have received multi-payouts, this depends on support having kept adequate records. Given the vast number of transactions in and out of Mt Gox, it may not be possible to correlate transactions to find duplicates, especially if a different BTC address was specified for the 2nd or 3rd attempt.
21. Even if customers could be traced, there is still the issue of trying to get the BTC back. This may not be practical as the legal costs would be substantial, and probability of success may be limited.
22. In summary, the coins have probably been paid out incorrectly to a number of customers, some by luck, but probably most by deception. However, this depended on seriously buggy software at Mt Gox, despite specific warnings from the bitcoin devs that it needed fixing, total lack of auditing of their customer deposit holdings, and lack of investigation into apparent technical failures and unusually frequent calls to support for "missing" withdrawals.
23. Given that it is very likely that internal controls were very, very lax - it is also a possibility that insiders may have exploited some of the bugs, e.g. support staff may have twigged that there was a potential exploit, and they may have been able to set up accounts under false names or where the legal paperwork had been "lost".