In the shadows, Riftborn sanctuary bug.

Hey Drift.  Just thought I should let you know that this help section, is for teaching people how to play the game.  Not to report issues with the game.  As a result, this is help area is almost entirely community driven and not really visited by the Dev's.  I'm not having a go at you, it's an easy enough mistake to make.  Hell, if I didn't know any better, I could've easily made the same mistake given how most every other website uses their "Help" sections.

If you'd like to report this bug, I suggest you report this issue in the following sub-forum:  https://www.games2gether.com/endless-space-2/forums/114-bug-reports

That's the proper place for reporting game bugs.

Hope this helps.

P.S.  Sorry I missed the final question.  See, I make mistakes too.  I can't answer your first question as that does "sound" like a bug.  

But the second question, yes that is very much intentional.  The Umbral Choir are not supposed to have minor pops of any kind.  The reason is, those minor pops have a really bad habit of popping up on your home system and taking up valuable population slots on your home system.  Blocking you from spawning new UC pops and as a result, badly limiting/hampering your ability to populate your valuable population slots with Umbral Shadows by upgrading Umbral Choirs.  Which in turn, significantly impacts your home system economy.  And on top of that, because you have no way of transferring pops between your home system and your sanctuaries, it means once you get even one minor pop, you're stuck with it, with no way to get rid of it, and no way to stop it from breeding.  The best you can hope for is if you're very, very, very vigilant, you could keep changing the pop spawn destination to ensure minor pops only spawn on sanctuaries and UC pops on the home system.  But this is a very manual and time consuming thing to do.  And that's only even possible, if you're lucky enough to notice that you got a minor pop early enough to stop it before it overrun's your home system.  As a result, the ability for the UC to have minor pops was completely removed because it ended up causing far more problems than it was worth simply due to the nature of the UC as a faction.  Plus it didn't fit in with the lore.