When you load a structure from a structure block that has waterloggable blocks (like stairs or slabs) in positions occupied by water (and sometimes other waterlogged blocks) before the structure loaded the water will stay. This means a stair (or other waterloggable block) loaded by a structure block will be waterlogged if the coordinates previously contained water prior to loading the structure. This can have some annoying consequences when reusing the same areas to load different structures.