What is the config to attach transparent face to object I'm blender noob.

In the bottom picture, that selected face detached to the mesh.

Let me know the config to attach that transparent face to the mesh like the upper picture.
Thanks for helping me.
The little black square is always at the center of verts which creates the face. So if you have concave or non-flat ngons then the square won't be located on the surface, but this isn't a useful thing.