Villages generate in different levels

When a village generates, it generates the different parts on different levels, making villages very ugly.

What I expected to happen was...:
I expected to find a village on the same level.

What actually happened was...:
I found a village with parts of it on top of a hill and some of them under.

Steps to Reproduce:
1. Generate a new world.
2. Find a village (Exploring or with /locate).
3. Find out that it's on different levels.