I am using the Children of Khan map (at least I think that's what it was, it is one of the "abondended" Starfleet ship maps), and had placed a few (Federation/ Generic S sized). It seems some of these containers, if just placed somewhere on the map, are partially inside the ground. It seems the height of the map and the standard height these containers drop to doesn't work. It's not a big effect, but it is visible.
I couldn't test whether it was the map itself or only the containers. It seemed that some ofthe larger containers and the container groups were sitting right.