[Plugin: Google Analytics Popular Posts] showing homepage as most popular post

First, do you have installed the latest version?

How to set the GAPI filter by WordPress Permalink Structure.
You can use regular expressions to filter expressions.

Default – An example of the default structure is https://www.sample.com/?p=123
GAPI filter ==> \?p=

Day and name – An example of the day and name based structure is https://www.sample.com/2008/03/31/sample-post/
GAPI filter ==> [0-9][0-9][0-9][0-9]/[0-9][0-9]/[0-9][0-9]/

Month and name – An example of the monthe and name based structure is https://www.sample.com/2008/03/sample-post/
GAPI filter ==> [0-9][0-9][0-9][0-9]/[0-9][0-9]/

Numeric – An example of the numeric structure is https://www.sample.com/archives/123
GAPI filter ==> archives/

Please visit Google Analytics Popular Posts plugin page for more information.