It's interesting to note that the transaction malleability issue was a known problem to MtGox at the very latest by November 2013. [1]
I know this first hand because I was on #mtgox at the time speaking to support staff trying to get some of my own coin out, which I eventually did get. I personally think that at this point they themselves were "wtf is going on?" about the issue and couldn't really explain what went wrong.
Between that time and now they surely must have understood the problem well enough to either use it as a "feature" or try and fix it, which they didn't.
I know this first hand because I was on #mtgox at the time speaking to support staff trying to get some of my own coin out, which I eventually did get. I personally think that at this point they themselves were "wtf is going on?" about the issue and couldn't really explain what went wrong.
Between that time and now they surely must have understood the problem well enough to either use it as a "feature" or try and fix it, which they didn't.
https://bitcointalk.org/index.php?topic=324918.0