Mt. Gox recently claimed they found 200,000 BTC that they'd lost track of. If their claim can be taken at face value, then I think it's plausible they may have panicked back when their losses first became clear to them in February, leading them to blame it on malleability even though they didn't really have a clue where their money went or why. They probably felt they had to tell people something, and saying "we lost track of >750,000 BTC for unknown reasons" may have been less desirable than blaming their problems on something tangible, like transaction malleability. Unfortunately for them, it turns out that they were wrong about that.
So here we are. All that's been demonstrated is that consumers currently have very little protection in this space, and that patio11 and others were right to warn people to be very careful with bitcoin.