Quoting Ron Lugge, reply 6
It's not a tetris 'minigame', it's a rather sensible restriction. Your city has to be one contiguous block.
Several buildings (lumber mill, fishery) don't follow those rules, and for the ones that do it really is like a tetris minigame as you find a way to snake your city out to the resource you want. I have cities with a single wide string of 1x1 buildings that stretches out far from the city until it touches a mine or fertile tile like 6-8 tiles away, I don't see that being very sensible. You don't see farms or coal mines in the middle of New York city.
That's why you build a pioneer and have the pioneer (or ironeer, if you're Gilden) go build an outpost (or whatever it's called) on the resource you want to harvest.
Edit: I should note that I'm not sure that you can do a pioneer for fishery/lumber, but for ore, horses (once the horse techs go in anyway), etc. you can.