I heard Reznor didn't like the way Manson was directing his music career and thought that he was beginning to sell out (which he kind of did after a while) and the two fought over the production of Antichrist Superstar. It wasn't a big thing starting off but some of Manson's band members felt the same way and didn't like the way Manson was monopolising the creative process of the album which led to a directive civil war of sorts.