When constructing a transaction, coins (transaction outputs in Bitcoin parlance) are gathered together from the sending account to cover the amount needed. When the transaction is confirmed, these coins can never be spent again. If they appear in another transaction, they will be recognized as spent and the new transaction is rejected. As your referenced article points out (just after the quoted section), MTGox sent out additional bitcoin, not the same coin.
The article correctly describes the malleability problem, and makes it clear that MTGox had to have been excessively lax on accounting procedures to allow this to go on for any length of time. I would add that it was MTGox's responsibility as an exchange software developer to understand and properly deal with the Bitcoin system. As the article points out transaction malleability was a known issue in 2011 (May of that year). MTGox had plenty of time to address the issue in their system. If they had been watching their accounts with any diligence, they would have known they had a problem and should have dealt with it then.
OK, I stand corrected. But you are totally picking a nit. Whether it is the same specific coin or two different coins couldn’t be less relevant. What matters is that the protocol has a flaw that facilitates double payment.