I'm trying to make a structure called the Ancient Complex generate naturally, which it does.. but...

It generates like normal, but whenever I add more then the Start chamber of the structure (like a gate that sometimes generates infront of an entrance, or a loot crate) it doesn't load this alongside the start chamber, but instead chooses from either the loot crate, gate or the start chamber to load..
(E.G: You have a start chamber and a end chamber, you want them to both load but when you find one, only either the end or start chamber load instead of both...)
How do I fix this? thanks so much everyone:))