I notice that some improvements have their tile requirements set to zero and the game doeskin appear to be handling this very well. If an improvement doesn't cost any tiles, then it can't be placed properly. When you select them in the build menu, it looks like they can't be placed. However, if you click on a location anyway, it'll be added to the construction queue, get built and begin to have an effect without actually appearing to occupy that tile. You can even build over it without disrupting the effects.

The most apparent example is the upgraded Kingdom Garden, which wreaks extra havoc due to being an upgrade to an improvement that does cost one tile. So if you have Basic Gardens built before researching Harvesting, they'll disappear. This also causes problems with demolition. Other improvements with this issue I know of are Lost Libraries and the Imperial Refugee Camp.

In the later cases, where the improvement in question is a special resource, the “not appearing to be built” issue results in the improvement not being cleared from the city's build menu, since it is still seen as unexploited.

I assume all this is simply a case of the tile requirements being entered wrong, not an intentional attempt to make those buildings not cost any tiles. But the idea of 0-tile buildings does give me some interesting ideas. Things like the space program from the Civilization series spring to mind. Maybe it'd be a good idea to make sure the engine can gracefully deal with 0-tile improvements for future modding purposes.