My day job involves regulatory reporting of OTC and ETD products, although I deal with the technical aspects not the business side so my comments contain some speculation (but the other responses to your question here seem better at that addressing those aspects).
A number of new regulations have come into place in the past few years to help prevent recurrences of recent financial scandals and meltdowns, and to ultimately bring stability to the markets, e.g. the Dodd-Frank Act (DFA) for US parties and MiFID/EMIR (and in the future MiFIR) for EU parties.
These regulations provide for e.g. daily and in some cases semi-realtime (30min) reporting of trading activities. Reports can also go to the counterparties who can dispute or verify trading activities.
Other countries, e.g. Russia, Singapore, Hong Kong, even South Africa are enacting similar pieces of legislation.
In some cases, the trade repositories (companies who accept trade reports) satisfy multiple supervisory bodies e.g. the DTCC will accept reporting under DFA, EMIR, MAS (Singapore), HKMA (Hong Kong) legislation.
Here is the speculative part: You can imagine this gives authorities a pretty good idea of who is trading what, what their exposure is and to who, etc. Because all parties are required to be registered with the appropriate regulatory bodies, I would think the alleged fraud at MtGox would have at least two obvious problems if they were subject to similar regulatory oversight:
(1) MtGox would be registered as brokers and wouldn't be trading parties, so at minimum it'd be very suspicious (and more likely illegal) to see them taking the other side of a trade (they couldn't report using a non-existent party for their side of the trade like they do here as that submission would be rejected since the party would be invalid, and they can't just not report because the counterparty buying the BTC will identify MtGox as the seller in its submissions; they also can't use a random real counterparty because that real party will dispute the trade took place)
(2) even if they legitimately took the other side of the trade (e.g. Mark registers as a trader) while cooking the books, I'd imagine they'd have to reconcile their audited books/bank accounts with their reported trading history, which would reveal fraud (by controlling the trading history they can claim anything; with a regulator, they can't control the trading history).
In effect, regulation of this sort would force all trading claims to balance out across all parties - where they don't, there would be an investigation.