No 404 on existing folders

Thanks for your reply. The RewriteBase is set to "/" in the htaccess of the subdomain.

I really have no idea why it does these things, pretty much..

Code:

RewriteEngine On
RewriteBase /
RewriteCond $1 !^(index\.php|assets|robots\.txt)
RewriteRule ^(.*)$ /index.php?/$1 [L]

thats the .htaccess in the subdomain.

This url gives a correct 404 error:
http://test.example.com/index.php?/application

but this gives the weirds symbols..
http://test.example.com/application

full log:

Code:

DEBUG - 2015-04-19 16:32:32 --> Config Class Initialized
DEBUG - 2015-04-19 16:32:32 --> Hooks Class Initialized
DEBUG - 2015-04-19 16:32:32 --> Utf8 Class Initialized
DEBUG - 2015-04-19 16:32:32 --> UTF-8 Support Enabled
DEBUG - 2015-04-19 16:32:32 --> URI Class Initialized
DEBUG - 2015-04-19 16:32:32 --> Router Class Initialized
ERROR - 2015-04-19 16:32:32 --> 404 Page Not Found --> application

and routing settings:

Code:

$route['default_controller'] = "store";
$route['404_override'] = '';

server error log shows this line when I browse to the page and get the weird symbols:

Code:

[Sun Apr 19 17:10:42 2015] [error] [client xx.xx.xxx.xxx] client denied by server configuration: /home/xxxxxxxx/domains/example.com/public_html/xxxxxx/application

So it says it is denying the access, yet it shows weird symbols,,