I feel for you Kori,I'm in a rather complex dynamic myself and its taking alot of talking to get through. When I met my primary he had just come out of a relationship with a mono woman and a month into things we found out she was pregnant. She decided to keep the baby and in the same breath did everything she could to try and get him back. Even though he is content with me,she is not happy that he has moved on 'with me'. there are times when I do feel like 'piggy in the middle' but the problems they had were there before I even came on the scene.
It may simply be that adding you to the dynamic of their relationship has brought out some underlying issues that may not have been apparent to you or even to them. You are really just the 'trigger' that led to this happening and like my situation,it may not have mattered who the third person was,it was more the 'situation' ..unfortunately because we are sensitive to other people's feelings we both feel guilty that this is somehow 'our fault' when in reality it may have happened anyway.