Mineshafts don't go through Aquafier Caves

An aquafier cave generated and split the Mineshaft it two rather than the Mineshaft going through it. 

What I expected to happen was...:
The Mineshaft should go through the aquafier cave

What actually happened was...:
Aquafier cave split the Mineshaft in two

Steps to Reproduce:
1. Random world gen

 

Seed: 877152199460335788

Coords: -520, -30, -250