Yea, I was going to disable the cycle on modular ships, it auto-rebuilds a slot if the module is destroyed, unless of course it's conflicting with cyclical build orders. But I just figured it would be less fiddly all around if the modules weren't individually killable, so I did that instead some versions ago.
What this sounds like is the ship coming out of the shipyard with the wrong build order or something, but I need a save (from before the shipyard finished the DN) to be able to tell.