I'm not sure if this is recent or not but I have found an incompatibility between Space Exploration Stuff and Cargo Ships.
When Space Exploration Stuff is installed the Ports (water based, Cargo Ships version of Train Stops) can no longer be placed against the Waterways (Cargo Ships version of Tracks). Also, Ports can usually not be places against Tracks but with Space Exploration Stuff installed they can.
I'm also posting this in the Cargo Ships mod discussion as I am not sure which mod needs the tweak.