So we have two separate instances of bases - one requires you to “Destroy the Spawnery”, second one requires you to “Destroy the Scylla”. Now, at the same time we can paralyse both of those units.
The problem is that when you paralyse Scylla, the map is successfully completed and you get alive specimen for your research. When you paralyse Spawnery, nothing really happens - game still requires you to kill Spawnery instead to finish the map.
The problem is that both actions are described in the same way - to destroy. We as players don’t know which units you require us to catch alive and for which you didn’t think of such approach. Thus we do our best to catch (them all) instead of kill to grab each and every necessary research (as this research on Phoenix Point faction side is really bad and we want to believe that we just do something wrong and our basic weapons/armor can still somehow be useful in the mid/endgame).
So those two tasks should be called differently to avoid misunderstanding - Spawnery should be destroyed, while Scylla should be eliminated (thus destroyed or paralysed, which should be explained to a player). Or just add a reason to paralyse and catch Spawnery - like some research in automatic elimination of Lairs on some level or something.