I think it happened in the code, when they switched to LevelDB.
It doesn't matter - whoever had that coins didn't bother to spend them on time, or more likely, nobody had them anyway.
And besides, he can always go to Gavin for a refund

You are throughly confused. We would never change the software in way that stole coin from someone, and no one would adopt the software if they did.
There were two instances of broken miners which created the same coins twice. Because of the way the software was written, with an implicit assumption that txids were unique, the second coins overwrote the first. The creator of those coins destroyed them, not anyone else.