I used to give descriptive names to directories that would each carry a main document, and associated materials like references, diagrams, etc. Since the directory already had a descriptive name, I used to name the main document like "-- paper.docx" so that it stays on top when sorting the files by name.

However, realizing the problem you have mentioned, I started giving descriptive names to the main document also, in most cases by re-using the name given to the directory, still adding the leading "--".