I just encountered this annoying bug in my latest BNW Deity game. This happened in the mid-late game where I had hammer built aqueducts in all my cities. I adopted all Tradition policies to get the 15% food growth bonus and faith buying GEs. This made the 4 aqueducts (free) in the first 4 cities that I settled. Then the bug occurred; upon my size 30 capital growing to size 31, the "Free" aqueduct did not store the 40% food! Only the 25% food was stored by the Medical Lab. The food required to grow to next pop is 419 , so we are talking about a lose of 168 with this bug! I need to do more testing later, but it seems that the completion of Tradition tree made the 4 aqueducts free but useless. Anyone else experienced this? It is very annoying since it is so food expensive to grow cities at this stage and losing the 40% carry over food in my top 4 cities is just ridiculous.