Google Analytics Not Using Proper Extention for WP pages

Hello. I am using WordPress 4.2.1 running Flat Bootstrap theme with include line for Google Analytics as so:

<?php include_once('/var/www/site.com/googleanalytics.php'); ?>

</head>

It is installed in a sub-folder as site.com/blog/.

The root index pages all use .html and .htm and all the blog pages use .php.

My Analytics stats show pages being visited as /blog/index.html etc.

How can this be when visiting a blog page as site.com/blog/index.html is a 404.

The default landing page in my analytics account is index.html. As shown here. The blog area is here.

I am not sure what to do with fixing this tracking issue. Thank you for any help.