Something consistent I have noticed with Autonomous Ship hullmods is often the mods highlighted in brackets don't work right away, often leaving it until way too late to do so.
[Retreat on severe hull damage] -
Spoiler
A pretty big example, eg; When a rare ship or ship you want to keep alive doesn't retreat until 2% hull remaining, while Harpoons or whatever missile is incoming, THEN they decide to retreat. By that time it's too late for them to retreat and they promptly suffer the consequences.
[Retreat on possible malfunction] -
Spoiler
Also another example, in a different instance, with ships that are prone to failures. EG; Afflictors, Shades, GMDA ships refuse to retreat until their engines die at 0% CR, in which then their defences are down or the abilities won't work
Just notifying for future notice. Although at the same time it may be on Alex's side as well. May be addressed in future patches.