I help you with the scenario: You get a message that you are now able to build a farm. You open the city screen to build it, like you build all the improvements before, but are unable to find the icon. You scratch your head and think that you either don't have the appropriate resources our you need to research something else to unlock the technology. Since it is not a pressing issue at the moment and the game continues without your farm, you decide to keep on playing thinking that you can try it again some other time.
That's where our minds diverge, when I get thwarted at the city I would've immediately clicked on the fertile ground tile to see what was up and search for more information. *shrug*
I didn't play the campaign, simply started with a random large map. In the beta it actually built those things from the city itself, it gets kind of awkward when you've got multiple cities since they are tied to the closest one. For example, you build 3 cities and research a tech in the adventuring tree that puts a resource in the middle of them. It would be hard to judge which city actually has "ownership" so you'd have to cycle through all 3 looking for the one that could build it. The new system is much easier to use and has more in common with every other 4x game that has resources out on the map. The only difference is you don't send workers to build improvements like the other games.
Galciv2 had construction ships and starbase to get the resources. Civ used workers and roads to build improvements on special resources. None of it was built directly from the city/planet.
I can see where your confusion came from, I can't really see how it lasted any significant amount of time. Even a little bit of logical investigation would've uncovered the solution.