I'm not sure if this is a bug, but last night I was in pvp on my bop, and on my team was a kling on the pre-order connie. The game doesn't let me use mine on kling side so I was curious how this is possible?
There's a known bug where people can get thrown onto the wrong team in PvP. I was in a 6v4 one time with a Raptor on the Fed side. It doesn't go away when he dies or anything, he's just on that team for the duration of the game.
This bug has been around since closed beta. There is a bug where people can get put onto the wrong team. So it wasn't a Klingon in a Fed ship, it was a Fed who was put onto the Klingon team. With this bug you can see 6 v 4 matches with that person on the wrong side. Its pretty rare, though.