This one is inevitably going to be difficult to diagnose.
If you can provide a video or other recording of ships doing something in a specific case you think they shouldn't be, then Alex has certainly looked at those before, but otherwise saying "They're not doing what I tell them to do" is hard to work with because if they stayed exactly where you told them all the time, other people (and maybe also you, and certainly me!) would complain "Ships are staying too close to the point and dying pointlessly". This is because AI is hard, and perfect tactical AI is neither plausible nor desirable (it'd usually be better than the player, for example).