i had smtn similar
yesterday i got quest "Increasing population" - gain 100 population
i've put 2 residences to upgrade from lvl 8 to lvl 9, and it didn't recognize it as done - the game was left open during that time
did it again (lvl 8 to lvl 9), and this time game was closed and it counted it torward the 100 population goal
3rd time, as i was still short of pop, game was closed too
after this quest, today i've got a quest for upgrading 2 buildings that were at least lvl 5 (Striving for Improvement)
so i've put my builders to work on my lvl 8 armory and my lvl 9 residence
both buildings are done, and game was left open again, but quest counted only 1 upgrade
this may be due to the fact it needs 2 of same buildings upgraded, but if so, then wording of a quest is completely wrong
this image was taken after i realized it didn't count any of the population it should have so i've started upgrade for 2nd time - you can see my armory all the way to the right (3rd one) still aat lvl 8:
http://prntscr.com/79s5kt
this image is taken after both upgrades of for 2 buildings lvl 5 or higher are done:
http://prntscr.com/7a61m9
just remebered it, and i don't know if this matters or not, but 1st time i've placed my residences to upgrade, i think they both had help effect - can't be 100% sure on this, and i think for the rest i didn't have it, but what i am sure is that with this Striving for Improvement quest i had 1 help (used on armory i think)