Why is my ragdoll messing up my animation?

I was trying to make a simple walk animation. So I just made the legs rotate forward and backward whoopdeedoo. So here is what it looks like:

As you can see the legs are going inside the "torso" a little bit, which I expected since I am just rotating it, but it is fine for me. Now as far as I know, you can use an animator on a ragdoll instead of instantiating a ragdoll upon death or collision to make a character. But I am just wondering why the legs are colliding with the torso (I know, it sounds dumb), which makes the animation break like this:

It doesn't stay still and soon falls off the platform :P but if I were to change an option on the animator while in play mode, it would fix itself back in place and the animation would work perfectly!

Any ideas?