I have had this bug happen to me this morning as well.
I researched the charged missiles tech for the assailants but turned it off autocast immediately. In the middle of a battle I turned it on autocast so that they would use it when needed reducing what I needed to mirco. After the battle was over, I turned the ability back off autocast. However, despite the ability not being used by me or the autocast system, the ships remained stuck indefinately, unable to move at all.
The only way I could get them to move again was by manually using the charged missile ability on every assailant, upon activating the ability, the ships could immediately move again.
The bug seems to be with the autocast system, for some reason when the ships autocast the ability, the appear to be frozen in place indefinately, long after the ability duration has ended.