I couldn't help but notice this when I tried building a ship in the shipyard.
My friend's destroyer sized ship came crashing through and ran itself into the shipyard so hard it took me half an hour to unglitch stuck it from the drydock.

This occurred after I had set the faction to treat neutrals as hostiles.
It took me a while to reproduce and retrace what is going on.

Basicly because any ship in a fleet is treated like an AI ship, his ship that unbeknownst to me was set to a fleet that was set to "Defend Sector". Decided the only course of action is to ram itself into the neutral ship that the shipyard spawns when making a new design.

This is a bug as far I can understand. The shipyard also works like a dock. And when docked ships take on the faction ownership of the stations faction owner. This does not occur with the ship that is newly set in design. As such it was marked as hostile.
Although due to its "digital" or "hologram" immunity status. None of the cannons fire. The ship just endlessly tries to glitch itself into the base creating horrible lag and worse actually managing to get stuck without being auto unstuck for hours.

If my understanding is correct the game is supposed to understand and treat shipyard design holo's as "fake" and as such the AI needs to be programmed to ignore the "fake" enemy contact.
Make of it what you will i'm just putting this out there.