Solution:
You just need to add a question mark after the index.php like so:
RewriteRule ^(.*)$ index.php?/$1 [L]
So the full thing (in your CodeIgniter .htaccess file is like:
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?/$1 [L]
</IfModule>