Most of the time in Drupal the clean url setting in admin section is now allowing to enable/disable the clean UR’s. It is totally unfocused.
This issue is not with the Drupal, this is because of wrong server configuration or .htaccess file. You can get rid of this issue by doing following steps.
1. Check the AllowOverride in httpd.conf is set to All
2. If you are using symbolic links then make sure that Options FollowSymLinks is uncommented.
3. Make sure that Options Indexes FollowSymLinks is on in document root setting section. If you have written MultiViews in-front of this line then you should remove it because it overrides the mod_rewrite rules.
4. Check .htaccess file is exist or not in drupal installation.