I have recently gone on a bit of an update spree and while doing that figured out I didn't have my vhost correctly setup to use the .htaccess files with "AllowOverride All"
However, setting that option completely broke my installtion, and I figured the culprit was an .htaccess file located in /nextcloud/apps.
I have the .htaccess file in /nextcloud, and AllowOverride All set in my virtual host for apache.
I also downloaded the latest release as a zip and checked on github, but I can't find any reference to an .htaccess file in /nextcloud/apps there, so I'm wondering if this is a remnant from a previous version that I just found now due to my misconfiguration of AllowOverride.