Mt. Gox knowingly traded non-existent Bitcoins for two weeks, filing shows
One theory is that Mt. Gox became fractional reserve some time in the past, either by losing bitcoins or by spending them.  Then they were unable to replenish their supply, so it was a matter of time before a bank run.The reason I tend to believe this scenario is because it's completely consistent with their behavior.  I watched them very closely, and there seemed to be no rhyme or reason for their behavior.  That is, unless they were missing everyone's bitcoin for some reason.  Then their behavior made perfect sense.In that scenario, Mt. Gox would have knowingly traded non-existent Bitcoins for far, far longer than two weeks.EDIT: I should mention that there's still no evidence whatsoever that malleability somehow led to the loss of >500,000 BTC.