When doing a full export we can get files doubled up appearing in export_info/files/ directory and also subdirectories under this directory.
It looks like if the file is used in a page / block it gets put here but at the same time the Files area of the user's Content section is added in with the same folder structure.
So, for example if I add a coverimage, img1.jpg, to a page it gets saved in the 'Cover images' folder in files.
When I export the user I get a copy of img1.jpg in export_info/files/ directory because of it's association to the exported page and another copy in export_info/files/Cover images/ because of it's relation to the files directory.
we used to export files in their directories to avoid name clashes - but now that we export files prefixed with their fileid we don't need to worry about that so we should export all files into export_info/files/ directory without bothering with the subdirectories and have the generated files html page point to export_info/files/ instead
The problem with this is if you have large files then it doubles up the size of the export zip which makes things take longer both exporting and importing