Sorry for the necro but I've just started having the same problem with my mod.
The AI ships will sometimes move all the way to another gravity well without using a phase jump. This takes a long time and obviously has a massive impact on how fast the AI expands their control.
Did anyone find a solution to this problem or know what causes it?
Update
Nevermind, I've fixed it. It was an ability I gave a capital ship that makes it act as an end phase gate point. It was somehow breaking the phase lines. I had to remove the ability to solve the problem.