I`m midgame. Still have to raid my first alien base to get alien containment. I finally found a citadel to raid by cheating help of a dev who told me, where the bases are. Guess what, I conquered the citadel and game still demands from me to raid a base. Thus I can not complete the game. BIG ANNOYANCE!
I tested it via console:
A nest counts as Pandoran colony, not the citadel.
This is clearly a bug and wasn`t there before Cthulhu.
I provide the savegame here:
https://workupload.com/file/mgAnwcQqAt9
Just evacuate the last soldier from the citadel and see: Still no Pandoran colony conquered.
You can, even when Citadels are out, new Nests and Lairs can already spawn.
I don’t know if it was there before Cthulhu or not, because in all of my campaigns I have conquered at least one Nest, mostly right at the start the first one, before Citadels spawn.
But yes, it seems to be a bug, so F12 is your friend 
That is no solution, sadly.
I used a known console command to reveal all colonies. There were only 2 nests and one citadel.
It takes a LOT of time, till a nest evolves into a lair. Time I feel, I don`t have now.
My population is now down to 45 %.
And again: It is an annoyance to find that colonies. See my other thread.
NO second or third team would help me, since haven attacks are so time limited now, that I have hardly more then 5 hours to arrive.
Take my word:
Before Cthulhu any colony counted. This is new now.