No actually, I meant the MtGox source code that deals with transactions. The malleability issue was known long before MtGox announced the exploit. It's possible that MtGox initially handled transactions correctly, but later introduced the malleability issue so they can blame their problems on that. Like I said before, I don't believe that's the case though.
Mark was the CEO, the lead developer, the lead business guy, the lead operations guy, and nearly everything else you can think of. He likely had unlimited power to doctor anything he liked, and probably in a way that would not make it easy for other employees to notice. Even if they did use source control, he could probably mask those commits.
Honestly I'm not even sure how many other technical employees they had. I would assume only a few.
Wow, this is something that's been bothering me for some time. Why didn't Mark grow the team? He evidently didn't have any employees, just a handful of contractors.