Registered just to inform you of this, as I can't believe no one noticed it before:
Completely normal, already built ships and bases are being turned into troll ships randomly whenever certain processing is done by the game. They are NOT erroneous AI designs, and they happen to the player too, even with all designs completely on manual.
So far, the only game event which I was able to pin-point with 100% certainty to cause the bug is when research gets finished. A portion of all existing ships (presumably only from the faction that had a research project completed) have random superweapons added to them. This all sounds like a game engine bug to me, probably related to the 256+ components issue.
Potentially, the number of empires+pirates in the game influence how bad it becomes. I'm playing with 19 AI empires so maybe I'm seeing this much more frequently than others here. Also, the game generated 25 pirate factions even though I had the slider on "few" (1400 Stars, 10x10 sectors).
I can provide a save if necessary, but it should be easy enough to reproduce. And someone else reproducing it on their install on a fresh game would rule out me having done something to mine that messes things up (which I don't think I did though).
I am also having a XXL ship size problem, mine seems to happen once a ship receives critical damage, the ship INSTANTLY gains over 1000 in ship size and usually ends up crippled in orbit. This also happened to my mining station just before it was destroyed, it bloated to over 4k size. This does not seem to change the hitpoints of the ships/stations though since they are still super easy to destroy.