Apparently MtGox had over 700,000 Bitcoins stolen. This equates to about 6% of all Bitcoin ever minted.
Take a step back, and think about what you would do if you ran a Bitcoin exchange that was valued at over $300million USD.
First, you would store the majority of your coins offline, in cold storage. That is exactly what www.coinbase.com does. When you have thousands of customers trading millions of dollars in Bitcoin every day, there is no reason to keep it all online. There is enough flow, that only about 10 percent needs to be liquid. It’s called fractional reserve banking.
Second, if you were in control of 700,000 Bitcoins, you would keep good track of the coins. MtGox is claiming the theft occurred in 2011, but they just became aware of it this year.
The whole thing sounds like an inside job. The coins were not hacked, they were most likely stolen. The Bitcoin system was not compromised, the employees were.