Hi @jasonwilde ,
you are not alone; have a look at this question from a fellow citizen:
https://cgcookie.mavenseed.com/community/12251-help-i-can-only-indent-one-circle-button
You have basically the same , or similar problem.
Maybe this helps; there are overlapping Faces like this (for clarity I only highlight 1 or 2 Faces at the time, I hope this is understandable; all 3 are the same piece):
