So my Mistah left and a couple of my other ferrikki are popping up as being inbred but they have no shared ancestry? Is this a glitch of some sort or does it just do that because I'm only breeding magic potions together?

Well, I looked at a couple of your Magic potions (not all, but enough). This one's grandfather on her mother's side is also her great-grandfather on her father's side. This one's great-grandfather on his father's side is also his great-great-grandfather on his father's side. And this one's great-grandfather and great-grandmother on its mother's side is also its great-great-grandfather and great-great-grandmother on its father's side. As for Mistah Left, his grandfather on his father's side is also his great-grandfather on his mother's side.