Sometimes OwnCloud includes “index.php” in the shared links.  It’s annoying and ugly.  Here’s some things to check:

1. Is mod rewrite enabled in the apache config?

   <Directory /var/www/html/owncloud/>
    Options Indexes FollowSymLinks MultiViews
    AllowOverride All
    Order allow,deny
    Allow from all
    <IfModule mod_dav.c>
     Dav off
     </IfModule>
    SetEnv HOME /var/www/html/owncloud
    SetEnv HTTP_HOME /var/www/html/owncloud
   </Directory>
   

2. Is the .htaccess correct?  The ###DO NOT EDIT### Section must contain this line (Generally the last line in the IfModule for mod_rewrite

   RewriteRule .* index.php [PT,E=PATH_INFO:$1]
   

3. .htaccess must also contain this block for the web app to generate URLs without “index.php”

   <IfModule mod_rewrite.c>
     RewriteBase /
     <IfModule mod_env.c>
       SetEnv front_controller_active true
       <IfModule mod_dir.c>
         DirectorySlash off
       </IfModule>
     </IfModule>
   </IfModule>
   

Those are my findings for making sure OwnCloud URLs stay pretty.