When a turret is manually docked (or entered from the mothership?) the turret spazzes into a very odd orientation that is only seen from serverside i.e. by other players, clientside the turrets appear completely fine, however block placing is touchy and AI cannot control the turret properly.
This issue is reset by resetting all turrets in the mothership structure menu (sometimes C on the turret barrel works), however this solution does not prevent the issue happening again with another or the same turret.
I do not remember what the state of this issue is in SP.