the changes to Collision in the Hovercraft cause them to collide with Cargo Ships Waterways, making the hovercraft effectively unusable once you start placing waterways. And this is relevant to island maps which are a big reason for getting the hovercraft in the first place
This was probably fixed in the latest Cargo Ship update (robot256 worked a lot on collisions), because I can't reproduce that bug. I can go over water ways with an hovercraft.