I am trying to confront Kellog, but no matter what I do when I enter the room with him everything automatically aggros and I cannot speak with him. I can kill him and do whatever else, but at the end I still have the quest objective to confront him and it keeps marking his dead body. I don't' know what to do, I am stuck and I don't want to use a console command to just skip this section of the quest because it seems like it would be important.

Did you search his body and take everything?

I searched his body, took everything and the quest didn't update. I still had confront Kellogg as a quest objective. I've done google searching and found out this is a common bug, but no one can agree on how to fix it. I've tried the various fixes/work arounds suggested by people online, but haven't found anything that works for me so far.