As I noticed today, when I had no settlers available and built a new well it said "Missing settlers" and wasn't producing. But as soon as I upgraded it to lvl 2 it was still displaying "Missing settlers" but the water count was decreasing and I actually had the production from this well.

I've searched about this bug on the forum and found http://forum.thesettlersonline.com/threads/15599-copper-mine-upgrade-while-not-settlers-employed?highlight=mine+settlers talking about the same bug but with copper mine in that case.

So I guess it might occur with other building, perhaps only "count building" like mines and wells.