Hello Jammerfar ,

You say "nets in the sea" and "Naval Links".
Looks like you are only placing waypoints but the AI needs a "Naval Area" marker for building naval factories.
Its the same like a expansion area but in water.

And like Sprouto said;
What AI are you using ?
Did you set "naval expansions" inside the game options to 1 or more ?
Are there amphibious waypoints from land to the naval area for engineers ?
In case you use my AI (AI-Uveso) is there enough build space for a naval area ?
(Did you know, my AI can autogenerate markers; Ready for copy & paste to your map script)
(My AI also has some debug functions to visual display how the AI is using waypoints and marker grids)

And if all fails, post us your unfinished map here, and we can do some tests with it.