Maneuver skills, Torpedoes, Boarding actions, Starpulses and more will sometimes become unusable even in circumstances when the ship has either never received damage or a critical strike.
I have not been able to reproduce this in skirmish mode, but its extremely easy to stumble upon while playing Eldar in multiplayer.
Here is a clip of this happening:
In the clip the ship has never taken any damage and is still at 100% HP, but can't use its maneuver skill despite it being off-cooldown.
This is not a display issue. When this occurs, it remains bugged for the remainder of the match, even through things such as Pyramidal Reconstruction.