So, specifically. I have a ship, I got the blueprint from somewhere online. It has a single turret, I eventually through play modified the ship adding several turrets, changing out docked shuttles etc. I converted the blueprint to a design for the shipyard. Everything you'd expect to work seems to be fine (building the ship, deconstructing, repairing, etc). Although when I took the ship out in the test area only the original turret on the blueprint appeared. Changes to the hull or internals appeared fine, just not the additional turrets I later added or docked craft I changed from the original. So I just left the test area, and when I got into regular space there was a bunch of "ships" spawned nearby -- inside a nearby planet as best I could tell with names like SalsaDoom_1440415435435_SYTEST or the like. I removed them with /despawn_all SalsaDoom_1440 all true. But as far as I can guess my ships turrets didn't stay on the ship, but ended up somewhere nearby in real space.
There doesn't seem to be a way to add attachments, despite what this (http://phab.starma.de/w/create_bug_task/) suggests? Anyway, I've included the blueprint in question here
Convert that blueprint to a design from a shipyard, load it. Note the turrets in particular, there should be two on top of the main hull, and one of the top and bottoms of each nacelle. Use shipyard to enter test zone, note turrets appear incomplete, partial or completely absent. Leave test zone, the missing pieces will be scattered around real space.