I gotta say the way the end of turn works is still sometimes pretty wonky. Maybe it's just because I'm used to Civ-like games where the enemies all take their turns sequentially, but the order of things really doesn't make sense. I hit end turn, the last of my units auto-move, then the enemies and beasties move, then I get techs and city-level-ups, then I get attacked by enemies...? And though I haven't sat down to document it explicitly, I swear it happens in different orders sometimes.
I know multi-threading is great and all, but c'mon. I shouldn't be wondering what order things are going to happen in every time I hit end turn.
I know this isn't strictly speaking related to your bug, but I felt like ranting.