Sadly that is not entirely unusual (resource spawning issues) and they are likely going to have to tweak that mechanism quite a bit.  In games like this, resource distribution, spawning, and the like is one of the toughest things to balance.

It was almost constantly being tweaked in Galciv 2 - since the same algorithm had to figure out a balanced way of distributing resources for maps of many different sizes, with different numbers of players as well as consider how to handle various techs or species advantages to resource distribution.  It's a similar balancing act for this game but is further complicated by the fact that most resources must be within 5 tiles of a city to be utilized.  So, they have to consider the fact that spawning resources further away than 5 tiles from a city or the potential site of a city makes them superflous.

That last bit is probably related to your dragon roost.  If it is too far from any of your cities I don't think it will link to any of them.