I haven't figured out what the issue is but I find that in some cases I do not get the option to build on a resource that is in my territory even though I believe I have the right techs (which I think I read we might not even need now).  Basically in my latest game I had an old growth forest right next to my starting position.  I was never given the option of building on it even though it was in my territory for the whole game.  Also a mine was close by and when my territory expanded over it I was expecting to be able to build a mine, but I wasn't.  And I had the mining tech.  I eventually ended up building pioneers to claim these resources but I don't understand why that was necessary.  Not sure if this is a bug or if I'm just not supposed to be able to build on these resources from cities.  Either way it needs to be more clear what I can and cannot build on, and why.