They're not complicated, they're just broken. "Destroy thargoid craft" when there aren't any in the alert systems:
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And now control systems are broken too, requiring somewhere between 5-10 times the amount of effort that they needed before update 14.02.
So we can't prevent the thargoids from taking unpopulated systems, nor can we reclaim any territory from them at all leaving them free to constantly retrigger invasions in the same systems that we keep defending over and over (and having to deal with the unreliable messes known as AX CZs in the process).
FDEV have succeeded in creating a war against bugs, but unfortunately not the octagon-shaped space-faring kind. The entire war should be put on hold until
all of this gets sorted out - we're supposedly already closer to update 15 / the next stage of the war than the beginning, and the fundamental mechanics still aren't working as intended.