Yes, a subdirectory of /var would be a good place to keep your files directory.
The filename above (1758-6135-1-PB.pdf) is still an OJS 2.x style filename. This means that the upgrade process couldn’t rename it, because the files_dir wasn’t correctly set in config.inc.php, or file permissions wouldn’t allow it to be renamed, or something similar.
Details on file permissions will depend on your server; see How should file permissions be set? for details.
Regards,
Alec Smecher
Public Knowledge Project Team