I don't know if this is a bug or not. I never used rally points before TA, but since I have been using them I've noticed some inconsistent behavior. A fleet rally point is supposed to make fleets out of all ships routed to it. In my experience it works as advertised right after being created, but the behavior becomes inconsistent after you load a saved game. After loading the game, it seems that the fleet rally point sometimes forms a fleet as it should, but sometimes ships that arrive at the rally point aren't formed into fleets. In my last two games it seems like about half the ships that arrive at the rally point aren't made into fleets.
Has anyone else seen this?