When resources are near or discovered adjacent to a city then upgraded to provide the resource the object takes up 4 tiles of the 50 tile max of cities. For example, I had a city that had a lot of resources that got put inside the city limits, by the time I was ready to specialize it to have Mints, market etc. I couldn't due to the resources taking up all the tiles. Did a test, put city all alone had 50 tiles of build room, put one adjacent to a fire shard and had 46 tiles of build room.
Not sure if this is intentional but it makes it a bad idea for now to build cities right next to the fertile ground or mines at the start if you want to get as much as you can out of the city.
Suggestion: If intentional, should instead make it so that any resource inside city limits not cost tiles, but can be upgraded further at the cost of 4 tiles