Any ideas/input?

Tried that in many ways, but can't get it working.  Here is a copy of the .htaccess file, what changes would need to be made (clearly input that code):

Options +FollowSymLinks

RewriteEngine On

prevents people from accessing anything with phpMyAdmin

RewriteRule phpMyAdmin - [F]

Remove index.php or index.htm/html from URL requests

#RewriteCond %{THE_REQUEST} ^[A-Z]{3,9}\ /(([^/]+/)*)index.(php|html?)\ HTTP/
#RewriteCond %{REQUEST_URI} !^/administrator
#RewriteRule ^([^/]+/)*index.(html?|php)$ http://www.mysite.com/$1 [R=301,L]

force canonical www if request is for non-www or has port number etc

RewriteCond %{HTTP_HOST} !^(www.mysite.com)?$
RewriteRule (.*) http://www.mysite.com/$1 [R=301,L]

redirect 301 /home.html http://www.mysite.com/

RewriteCond %{QUERY_STRING} mosConfig_[a-zA-Z_]{1,21}(=|%3D) [OR]
RewriteCond %{QUERY_STRING} base64_encode[^(]([^)]) [OR]
RewriteCond %{QUERY_STRING} (<|%3C)([^s]s)+cript.(>|%3E) [NC,OR]
RewriteCond %{QUERY_STRING} GLOBALS(=|[|%[0-9A-Z]{0,2}) [OR]
RewriteCond %{QUERY_STRING} _REQUEST(=|[|%[0-9A-Z]{0,2})
RewriteRule .* index.php [F]

#RewriteBase /
RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
RewriteCond %{REQUEST_URI} !^/index.php
RewriteCond %{REQUEST_URI} (/[^.]|.(php|html?|feed|pdf|raw))$ [NC]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . index.php [L]

I'm having some duplicate content issues with Google.  I've already got my .htaccess file working just fine as far as I can tell.  Rewriting works great, and by using the site you'd never end up on a page with /index.php.  However I do notice that on ANY page of the site you could add /index.php and get the same page i.e.:

www.mysite.com/category/article

and

www.mysite.com/index.php/category/article

Would both return the same page.  How can I 301 or something similar all /index.php pages to the non index.php version?  I have no desire for any page on my site to have index.php in it, there is no use to it.  Having quite the hard time figuring this out.

Again this is basically just for the robots, the URL's the users see are perfect, never had an issue with that.  Just SEOMOZ reporting duplicate content and I've verified that to be true.