Reasons for your worsening stomach problems on a paleo/ low-carb/ ancestral/ gaps/ etc. diet

With all these success stories about people feeling better on various diets, I think we forgot the people who sometimes feel worse. Probably because those people give up and don't stick around. I'm known many people who have adopted paleo, primal, ancestral, low-carb, gluten-free, or whatever diet. And instead of feeling better, they have all kinds of problems, particularly stomach problems. 

There are many reasons why this happens, here are a couple I tend to come across:

Can you digest bone?

 Possible too gross for some, via John Hawks, this article that mentions a most interesting experiment mentioned in an article on strange science:

Beating IBS

 Mark Sisson posted a link to a sad essay called IBS Is Why I'm Still Single. Every day I'm able to eat and live normally, I am so grateful. You see, most of my life I had painful stomach problems. When I was four I remember crying in the bathroom.

The Gut-Brain-Skin Axis

 When I was a child I was obsessed with several things, but two of them were Motown Oldies and aliens. I also had a bad habit of hearing things rather strangely. A good example would be the song "It's in his kiss" by Betty Everett. For quite some time I thought it was actually "It's in his skin." Since I was also into aliens I kept thinking about would would be in his skin besides baby aliens? I must have seen that scene from Alien when my mother wasn't looking...