Running 12.04.
I have apache up and running well for my root folder and subfolders which I create, but installed owncloud and the subfolder it created 404s even though I can see the folder from the server side.
So,
[domain] works fine
[domain]/whatever works fine
[domain]/owncloud (created by the installer) 404s
I don't have any aliases or sites defined in /etc/apache2/apache2.conf or /etc/apache2/sites-enabled that speak to that subdirectory. I don't have an .htaccess in the folder that is causing a redirect. I did ls -l to look for symlinks, and found none.
The directory is owned by www-data:www-data and has permissions drwxr-xr-x.
When I create subdirectories myself they resolve fine.