Don't place warehouse buildings in the settlements you want as cities later (those with high production, or with a lot of ressources). Even thougth those warehouse could have given you some food/production, they are based on rural tiles, which will be eventually transformed into quarters... So by mid-game you will get pathetic yields, but an eternal building you can't get rid of.... Warehouse buildings are a city trap! (well, except for fishing quay, there's not a lot of buildings on water...^^).