Not sure what the name of the structure is, but here is a picture of it
https://gyazo.com/ca458c858e0c7d184c6ed52994d93cfb

It has a deep basement, with one of the walls looking like this
https://gyazo.com/950735506b0c03f346806f71d22a6f19

Are you using Optifine? Have you tried reloading the world?