I don’t get it either. I have a site on Dreamhost and it has almost NO content and NO plug ins yet. My son runs a growing and very active tech blog on Dreamhost as well. I assumed the problem may be that it is a spider issue since he had so many. We pretty much shut them down and the 404 errors are rampant on the back end. wp-admin.
Now my site is as I said, new and baron. Nothing but the theme. I too am getting file not found 404 errors just driving around on the backend. So it has to be either Dreamhost or 3.41. I suspect its WordPress.