This is by no means a giant thing, just something that someone with mildly OCD tendencies could be annoyed by. 
When I set up my Chapter folders for my novel, I put five files in each folder (because each chapter was going to visit five POVs): A, B, C, D, and E. And instead of re-creating them for every folder, I Simple Duplicated the five files and carried the copies down to the next folder.
When I was done with this, I realized “B” had a space in it, because the file always showed up with the icon with writing on it, indicating text. So I went through and deleted the space out of every “B”, so that all the files would show up as empty.
When I quit Scrivener and reopened it, all of the “B” files showed up as having text again. No matter what I do, in fact, they always show up as having writing in them. I don’t know how I did this! But apparently I can’t make it go away. (So I suppose I’d better go write some text in those files, to save myself the mental anguish.)