I added the buff from the Ion Blast that disables phase jump to the Hyperspace Disruption buff and then gave my carrier the Hyperspace Disruption ability. The range on it is relatively low and they could have easily moved outside of the radius also to retreat. Or like I said they could have just destroyed the ship and then retreated. I don't know how the AI thinks, or how it's supposed to think, but shouldn't it at least have some "fight or flight" instinct and when it can't 'fly' it should fight.
Hmmm... I do see your point in that the AI should know how to deal with different situations, but I guess it will be expanded in time to cover alternative scenarios...
The behaviour I have witnessed in-game from ships charging to jump in the presence of a phase jump inhibitor is that they will just sit there waiting to jump until they finally charge up and get out of there.
Similarly with a ship hit with an Ion blast, it will sit there waiting to jump when it wears off (well, it has no choice really, the craft is completely disabled until it does).
I guess the thing is the AI is currently programmed that if a ship is trying to jump out of a gravity well it will sit there trying to do it until it succeeds, because anything that is effecting it's jump ability was designed to be temporary, or simply extends the time to charge for jump.
Technically, a jumping ship in effect of a phase jump inhibitor should be able to move to a point outside of the effected region (if it can find one) but it currently does not do this from what I have witnessed (probably because it has already starting charging for jump, and will not break from that charging to find a better jump point if it exists).
I would imagine that a ship only knows it can't jump when it goes to jump, and it seems that if it can't jump it just waits till when it can.
As I said at the start, you are right in that it sounds like an area that could do with improvement, but i'm not surprised it works the way it does. Normally the disabling of phase jump (total disabling via Ion Blast) is temporary, and also comes with complete disabling of the craft. Also, this effect can normally only hit one craft at a time (instead of an Area of Effect thing).
That's the thing about human modification and emergent use of an application I guess... Someone will do something that is outside of the design characteristics and highlight an area for improvement.
As for the comment about "fight or flight" instance... I guess the thing is you already triggered a fight or flight instinct, which made it try 'flight' in the first place. The permanent inability to 'flight' (AOE) seems to be something that the AI cannot cope with at the moment.
The other point you make about how the craft could have destroyed the ship then retreated... I can see no manner in which the craft that were trying to jump would have been able to identify the carrier you modified as a higher priority target than any others, even if they did want to attack. Adding an ability doesn't mean the AI suddenly will be able to determine where it is coming from, or that it is not going to wear off...
I guess it is another modding question a little, but is it possible to update the AI yourself? I would suggest it would be necessary to update AI to allow it to 'see' the hazard your modded carrier poses, so that even if a 'fight' response was able to be evoked when they cannot flee, it would know what to hit first, to allow the 'flight' response again...