A couple of odd behaviors:
1) I think this is a known issue: if you have a saved ship you designed with more equipment attached to it than your current hull mass would allow, you can build the ship anyway in a new game.
2) If you make older, game-generated ship models obsolete, then "Ship Graveyard" anomalies that should have ships will be empty.
3) I designed an early-game survey replacement vessel for exploring Ship Graveyards, and used Duratanium and Thulium in its construction. I shouldn't be able to build it until I've mined for these items, but if I try to build one in the new game without mining, it goes ahead and lets me! It notes my resources as "-1."
4) Found a Survey vessel in a Ship Graveyard; again, I didn't have the mines yet, so it marked it as -1 resource.
Hope that helps!