There are different layers, they are layered on top of each other, your base layer, the lower or first one, is for walking tiles like full-grass tiles.
The second layer and third layer are for tiles that you want to sit on top of the base tiles, or tiles that are not full squares.
The reason why you have three instead of two is encase you want to put down some flowers on top of the grass and then have a tree on top of the flower patch.
Go into the first layer then put down grass, go into the second layer and place your tree. If you still have the problem then you haven't set up the tiles correctly.