Quote Originally Posted by Geoff View Post
Learn how to fix it or you will most likely run into the same issue again, and you will be right round in a circle. If you don't know how you caused it when you modelled, then chances are you most likely will repeat the problem. Learn from your mistakes
I can't fix it, I don't know why it happened. I have seen Freecad do it before on much simpler things where you just have a couple of things intersecting sometimes it just makes a real cock up of doing the subtraction.

Time to learn Blender methinks.