Did this happen after you researched Harvesting? Several others have reported such an issue.

I've noticed the same thing.  Before you research Harvesting, Gardens take 1 tile space, and you can place them on the green squares, as you please.  After you research Harvesting, the tooltip shows that they require 0 tile spaces, and you cannot choose where to place them.  Zooming in/out shows that they are  built on top of some random structures.  Also, if you build one before the research, it merges in with the city somewhere, when you research Harvesting.

Also, the icons on the cloth map usually fade away immediately, but if you zoom out (to the cloth map), and then click the 'Build Structures' button, they all show.  But not if you are showing the 3d map, click the 'Build' button, and then zoom out.