I've noticed that if you place something onto a rural tile but then cancel it before any work is done, the game basically won't let you place it anywhere else because it's already freed up the rural population to be placed elsewhere.
It doesn't actually tell you that of course, you have to figure it out on your own. However, I did notice that for a standard building, the target tile has two blue circles at the bottom, though I'm not sure if that happens consistently.
I didn't test if you could back out of it by placing a growth population onto the tile to revert it to rural, but I suspect the tile is in a weird halfway state and it won't work.
If you place the canceled building on the tile, the problem goes away. I didn't test if placing another building on the same tile might make things right, but I suspect that has a better chance of success than trying to revert it to rural.
Edit: This only happens when the building is at the top of the queue. If you're really paranoid, You can queue up a research project at the top and then the building after. It will ask you to confirm turning the tile urban, but won't do so until the building is at the top of the queue.