Prevent nginx from serving files that start with a period or tilde will help.

    # prevent hidden files from being served and logged
    location ~ /\. {
      access_log off;
      log_not_found off;
      deny all;
    }

    # prevent tilde files from being served and logged
    location ~ ~$ {
      access_log off;
      log_not_found off;
      deny all;
    }