In one moment of game i noticed a very strange jump by resource income and after some turns i tried to figure out what was this. I keep in mind what this jump was especially in turn with 30 collection bonus of Umbral shadows, so i start to investigate whats going on and found that the bonus also applies to some other systems. For example: we have a population collection bonus, which looks like this: 

and we have 276.3 allocated Bandwidth

so we have proper numbers with tier 2 and tier 3 collection bonus with 44 umbral shadows - 772.6 (44*5+276.3*2=772.6) which is working as it should be to our home system

But i found, what exactly tier 3 bonus "+2 FIDS per allocated bandwidth" applies to some other systems with sanctuaries, like on screenshot below. Marked systems takes bonuses from Umbral Shadows tier 3 bonus, for example here is 1 pop-up message with 552 bonus industrial

I tried to figure out, whats the problem and why it happens with these systems only. And i remembered what all of this marked system was in control by minor factions which was assimilated. In Olvaldi was Sisters, in Farver was Eyder, in Pyxis was Kalmat and in Ugaro was Niris, i will attach save from early game, where almost all factions not assimilated and stays right where i remembered (excluding sisters - they already was assimilated) Mark problematic systems on screenshot below to simplify their finding in game.

So, i suppose what problem in game rule where tier 3 bonus applies not to your home system or only to systems with umbral shadows, as it should be (like tier 2 collection bonus) but to all systems, which counted as homeworld to somebody. As an example of this theory - i tried to settle system Isso, which was homeworld to Illo faction and it worked again. This system received same bonuses, like problematic systems, you could try it from attached saves.
I guess this is not feature of mechanic, but bug, so i posted it there especially after news about polishing patches to endless space, hope this is not hard to fix. Love your games guys, keep it up and good luck with humankind :>

In some places you could find cyrillic words because game was started with Russian Localization and was turned to original English in attempts to find original texts of effects, to be more accurate in conclusions.

Turn 134 save: BUG TESTS (CHOIR 3_1).sav

Turn 30 save Choir (BUG TEST 30 TURN).sav