Category Urls Showing Up With "index.php" Suffix In Google Analytics

Last night I changed the category structure of my site. I reduced the number of root categories and added sub-categories. The URL structure I chose is:

However, when I look at Google analytics, all of these category URLs are showing up as:

Does anyone know why, and more importantly, does it matter?

In my browser the URL structure shows up properly, without the “index.php” at the end.

Formerly my category URL structure was:

Any and all help appreciated.