AI fleet ships will attempt to pathfind around each other or asteroids being thrown at them, but if a ship's path in a movement order is obstructed by a non-fleet ship or immobile structure they will slam right into it.
Also, they may attempt to fly directly through a ship to access a pickup area that is not in line-of-sight, even if there is another available.
(Suggested fix: If no docking points are unobstructed, orbit around mothership checking periodically until line-of-sight is obtained; will result in glitchy behavior but better than now)