I completed a mission and had 2 bodies found but was unaware of this during the mission. I have a check next to "Ghost (Never Detected)" but want to make sure that I will still be eligible for the Ghost trophy or if I have to restart and make sure those bodies aren't found.

Dont take my word for it but I would say that you get ghost as long as you are not detected. Also its ok if you get detected in a neutral area like when you go to a certain party. The game will say you are in a neutral area.