This is my entire mod_rewrite condition:

<IfModule mod_rewrite.c>
   <Directory /var/www/>
    Options FollowSymLinks -Multiviews
    AllowOverride None
    Order allow,deny
    allow from all

    RewriteEngine On

    # force www. (also does the IP thing)
    RewriteCond %{HTTPS} !=on
    RewriteCond %{HTTP_HOST} !^mysite\.com [NC]
    RewriteRule ^(.*)$ http://mysite.com/$1 [R=301,L]

    RewriteCond %{REQUEST_URI} ^system.*
    RewriteRule ^(.*)$ /index.php?/$1 [L]   
    RewriteCond %{REQUEST_URI} ^application.*
    RewriteRule ^(.*)$ /index.php?/$1 [L]

    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d
    RewriteRule ^(.+)\.(\d+)\.(js|css|png|jpg|gif)$ $1.$3 [L]

    RewriteCond %{THE_REQUEST} /index\.(php|html)
    RewriteRule (.*)index\.(php|html)(.*)$ /$1$3 [r=301,L]

    RewriteCond %{REQUEST_URI} !^(/index\.php|/assets|/robots\.txt|/sitemap\.xml|/favicon\.ico)
    RewriteRule ^(.*)$ /index.php/$1 [L]

    # Block access to "hidden" directories or files whose names begin with a period. This
    # includes directories used by version control systems such as Subversion or Git.
    RewriteCond %{SCRIPT_FILENAME} -d [OR]
    RewriteCond %{SCRIPT_FILENAME} -f
    RewriteRule "(^|/)\." - [F]
   </Directory>
</IfModule>

It is suppose to allow only access to mysite.com(/index.php|/assets|/robots.txt|/sitemap.xml|/favicon.ico)

The error was noticed with: mysite.com/sitemap vs mysite.com/sitemap.xml Both of these addresses are resolving to the xml file while the first url should be resolving to mysite.com/index.php/sitemap *

For some reason mod_rewrite is completely ignoring the lack of an extension. It sounded like a Multiviews problem to me so I disabled Multiviews and it is still going on.

***And then a different rule will eventually take the index.php out, I am having another problem with an extra '/' being left behind when this happens.

This httpd file is setting up for my codeigniter php framework