When restoring data with a Mac Backup Client (SE or DL), a warning is seen in the restore log similar to the following:
Message: 09:34:08 Restored /Users/John/Downloads/my_Image.png
A limitation in the Mac Backup Client along with permissions allowed by the operating system for a user running the application prevents the Backup Client from modifying permissions.
The warning can be ignored because the files are restored regardless. However, permissions are not restored. (Bug 8168 has been logged to address this limitation.)
To re-set permissions manually, follow this guide as per Apple Support: Set permissions for items on your Mac