Basically I've made a directory called 'test' in /home/(site)/public_html and if I go to (site).com/test or www.(site).com/test it gives me a 404 error.
I replaced all -Indexes with +Indexes and now I can access it from www.(site).com/test but not at (site).com/test.
I also got Virtualmin installed
EDIT; SOLVED: In webmin > Servers > Apache Configuration I went to the Any on port 80, and changed the path from /var/www/html to /home/(site)/public_html