It's possible Mt. Gox had the same thing happen and didn't notice. As I understand what they're saying, Dwolla just changed the status back to unpaid and took the money without any notification. If you weren't looking for something like that, you might not notice until some time later when you tried to balance the books.
It's also possible Mt Gox has had the same thing happen and hasn't talked about it publicly. Based on the reasons they gave for their French bank cancelling their account, we know someone's tried this with Mt Gox SEPA transfers using stolen online banking information, and since SEPA transfers are definitely reversable it's very likely they lost some money from this happening, yet they haven't said anything.
It's not like Mt Gox are exactly the most honest and straightforward organisation; in the past they haven't admitted to anything that wasn't already obvious.
]How does it protect them against fraud? They've still been defrauded out of exactly the same amount of money. They've just additionally defrauded one of their customers. If Jack steals $10 from me, and I respond by stealing $10 from Joe, I haven't "protected myself" against Jack. I've just victimized Joe.
It protects them by fraud by transferring the risk to the party that actually has control of it. Remember that it was TradeHill that chose to offer the high fraud risk service of selling untraceable cryptocurrency rather than something lower risk. Also, your analogy is bad. Dwolla are effectively a middleman - the reversed transactions to TradeHill were carried out at the (fraudulent) request of the person who originally transferred in money that was reversed, using that money. It's more like if Jack gave you $10 of stolen money to give to Joe, and then the victim came and demanded it back.
However, since it is clear that Dwolla transactions are in fact reversible (contrary to their claims)
Did they actually claim this? I've seen them advertise "no chargebacks" as a benefit, but that's still technically true - chargebacks are considerably nastier than merely reversing the transaction. In fact, I'd always got the impression that Dwolla transactions were reversible based on their promotional material.