I also got a second copy of the LE. It also happened back when Sins of a Solar Empire was released. At that time I hadn't spoken out, I just assumed I got lucky, but now it's a pattern.
Both time I had pre-ordered the digital copy, and upgraded it to a physical copy (don't remember if SOASE had a limited edition), since I wanted the bonus. My guess is the original purchase and the upgrade are treated as separate orders, the first for the online edition + LE, the second for the LE.