I am using CodeIgniter php framework for built fast and secure PHP applications. It is really bad at SEO default. So i have to make a little work. But when you use the famous htaccess trick you will get tons of 404 errors. You have to add directory or file to prevent 404. See how:

Standart .htaccess file

RewriteEngine on
RewriteCond $1 !^(index\.php|img|en|font|banners|uploads|fancybox|userPictures|images|css|js|robots\.txt|Common.xsd|facebook) *dosya ve klasörler buraya ekleniyordu
RewriteRule ^(.*)$ index.php/$1 [L]

I have to add files or dir to RewriteCond. At the and i found a htaccess fix .

# Enable Rewrite Engine
# ——————————
RewriteEngine On
RewriteBase /

# Redirect index.php Requests
# ——————————
RewriteCond %{THE_REQUEST} ^GET.*index\.php [NC]
RewriteCond %{THE_REQUEST} !/system/.*
RewriteRule (.*?)index\.php/*(.*) /$1$2 [R=301,L]

# Standard ExpressionEngine Rewrite
# ——————————
RewriteCond $1 !\.(css|js|gif|jpe?g|png) [NC]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ /index.php/$1 [L]