I saw this bug first on youtube, presented by Arumba:

 

What it comes down it, is that the shipyards 'manage' screen does not check for capacity when deciding whether vessels are build-able.

Yesterday I was playing a game as a custom faction, the Frederation, which uses the Terran tech tree and ship style. I focused capacity research (as usual) and designed a late-game constructor ship with 4 construction modules.

Today, I started up the Campaign (which has the Terrans as the player faction), and just built my first shipyard. I can see my user-designed ships, at least in so far as that I have the tech to produce them...

But as you can see, the designer is showing all ships which are technologically possible even though they are not physically possible given the size of the hull.

Nevertheless, these ships are also shown and - more problematically - buildable in the 'manage'/doubleclick screen of the shipyard:

Interestingly, they are *not* build-able from the quick-build menu:

 

I wonder if the AI will have access to these super-ships too...