that is not a bug.
you probably took the AIs homeworld and "defeated" it, of course the remaining planets, ships and structures will remain in the game to be shot down and taken, but it won't rebuild or attack anymore.
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there is 1 bug i encountered with entrenchment 1.01 with the vasari missle defense platform, the research where it can disable all passive regeneration sometimes effects ships forever.
i was vasari myself finishing off another vasari with a badly hurt level 8 carrier capital ship in my fleet.
it had 608 HP left and 17 AM while it got the "regeneration disabled" effect from that platform.
after clearing out all remaining platforms and 5 minutes later that same ship was still stuck with 608 HP and no regeneration at all.
it didn't matter because after that i won the game but in any other case my cap ship would be dead unless i retreated it back to my repair-platforms.