Another thing I've found adding docks, cities & industry:
I had 5 types of scenery around Tokyo harbour, this included 2xdocks 2xcities & 1xindustry. I tried to add a 6th dock but I kept getting a crash so I gave up, then I had the idea of adding another dock further down the bay at Yokohama... this worked.
So there must be a limit to the amount of scenery you can have in a certain area.
But as MLF mentioned above, it is a pain keep having to go in the mission editor to get the correct co-ordinations then open the sim to see if it has worked and it is where you wanted it, then back to the editor again to add more or make a correction if needed.