I have noticed this bug for the first time in version 1.0X. I have not witnessed it within previous versions.
Quite often, some of my fleets at the start of a new turn have 0 movement points. For example, the ship info panel displays: 0/7 movement points left, despite me not having moved the fleet yet. Nor is the fleet on any autopilot course that it could have used up its movement points (this happens at the end of turn anyways). I can then hit end turn as many times as I like, and each consecutive new turn, the fleet continues to have 0 movements. In effect the fleet is immobile. Note, this bug seems to be related to fleets only, not individual ships.
The only work-around I have found is to disband the fleet, hit end turn, and the next turn I'm able to move the ships individually. However, If i choose to reform the fleet, the bug returns. The bug affects all fleet types, not just fleets with ships of mixed ship types, but fleets with identical ship types/designs as well.
I've spoken to several people in the #galciv channel on irc.stardock.com, and they too have confirmed they've witnessed this bug.
I'm attaching my savegame for reference and verification of this bug for the developers. Try moving my Iconian Fleet 145 (located to the west of planet Bond III). It is immobile, regardless of how many times you press end turn.
http://def.qwplayers.org/galciv2/QuickSave.sav
P.S: I believe I have found a way to recreate the bug. It appears that the problem arises, when you save a game when a fleet has 0 movement points, for example, at the end of a turn, and then you CTRL+L and load the saved game, that fleet seems to be permanently immobile, regardless of how many times you hit end turn. However, this is not the only cause of the problem, because it happens alot more often than just that, and without any game loading.