Wall Street Journal got an interview with Mark Karpeles. And this answer was interesting:
Q: What were your mistakes?
A: Security. Not just security on the system, but in the office. We had some cases where a stranger sneaked in and took things away. We also have at least one former employee stealing the company’s data.
If you got hundreds of millions of dollars in bitcoins lying around your office, people will try to steal those bitcoins. And if your security is not adequate to the task of protecting this kind of money, someone will eventually succeed in doing so.
It could have been worse, though. There could have been a violent robbery with the same result, but leaving MtGox employees injured or dead.
We also learn from the interview that a police investigation is going on. Eventually, that investigation may come up with information on what exactly happened.