It seemed like some parts he just threw in there for no reason. Like, he wanted to have a sex scene, so he threw in a prostitute, which was really irrelevant, and he wanted a few f-words in there, so he threw in a random punker, whose personality really had no impact on the overall story. That annoyed me -- I don't mind swearing and the like in literature if it's for some purpose, be it artistic or to help set a tone (like, I just read Catcher in the Rye, and his constant use of "goddamn" helped a lot with the angsty feel), but I think it's ridiculous when an author puts it in just to put it in.
I kind of enjoyed Digital Fortress, but, like you said...