Ok so here's my problem.
I have created a virtual host to test come CMS systems and I have noticed that some systems work (Wordpress) and some systems don't (grav, pagekit). The ones that do work behave like they should and the ones that don't work behave like I have an empty folder and the website shows the default nethserver intro site.
So basically the server acts like I don't have any files in my folder even though I do.
I have tried changing permissions and it didn't work and both CMS systems that don't work have an index.php file included (in case it would need one). The added index.html file gets displayed (when I add one) so I don't know what could be the problem.