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I'm the developer for a website with Analytics already set up and the Default Page is set to index.php. This is because it is built with the PHP Framework CodeIgniter.

I'm confused about and have questions about a few things...

GA shows /index.php as the main page, then for about 10% of the results of inner pages it will append index.php to the end of the URL and nothing at the end of the rest of them (no trailing slash). Why is that?

And my main concern, WordPress is installed in another directory (/articles) and GA shows and /index.php on every page for WordPress. Of course, those pages come up as 404s if I put them in my browser with the /index.php. Are visitors seeing those 404 pages or is GA just adding that /index.php because it's set as the Default Page?

What's the best way for me to set this up in GA under these circumstances?

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AFAIK Google Analytics takes your pages URL as it was requested by browsers, just like it's shown in browser's navigation bar, and Google Analytics takes it on the client side because it runs using javascript.

Have you checked how your URL's are inside your page's html? Maybe there are some inconsistencies, maybe few of them include /index.php and others do not.

What about your htaccess? is it configured to remove index.php?

If you want to check all your website's errors you can sign up for Google Webmaster Tools, register your website, and let it show your website's problems regarding "Crawl Errors" (that's the section you must watch). There will be 500, 400 errors if found by GoogleBot. Reporting will not be inmediate, and it will not tell you about problems before you register your website. But it will help you a lot starting from that point.

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