I noticed that when i start to built ''one per empire'' building/improvement on more than one planet at once and it is finished the other planet(s) still have this improvement in queue and it doesnt disappears until you cancell it. That way I once have blocked further development on one of my systems until i figured out that it is ''one per empire'' and i must delete it from its queue to allow further improvements. I think it should be removed from building queue automatically in such  situations or there should be at least notification/tutor hint when such a thing happens.

It arent big flaw but I wouldnt mind if it gotten improved.

I concur! It's mildly annoying, and was the same in Endless Legend - the worst when it happens in the crucial and/or micro-heavy segments.