Apache multiple sites, one works, other doesn't

Maybe the problem is not the config. Many other modifiers (including .htaccess) impact the server response.

To isolate the problem, use the failing website config file but use the working website directory path and see if it works.

So the problem was that for SSL the config file above wasn't being used. I've found the problem by listing the sites enabled sudo apache2ctl -S which returned:

port 443 namevhost site2.example.com (/etc/apache2/sites-enabled/site2-le-ssl.conf:2)

Which is a file created when setting up letsencrypt. I fixed the issue by disabling the config file, sudo a2dissite site2-le-ssl.conf.