Hi,
That is because of the actual resulting size of the terrain.
If you select the terrain layer, go to the Inspector and set the wireframe alpha to 0.3, then press the '7' key after making the viewport the active window. this triggers the wireframe display render setting.
This way, you can see each polygon on the terrain layer.
Then, also in the layer attributes of the terrain layer, play with the U and V subdivisions to adapt the resulting polygon size of the terrain.
The issue in general is that if you align shapes to the terrain and the other way 'round is that only the individual points are moved up and down, but the edges between the points still may intersect the geometries. So what I usually do is make an offset of 0.5 meters to prevent this as well as possible.
The terrain tools need some updates, we have this on the wishlist already quite some time. 😕
Makes sense ?
Matt