GetPaid saves invoice notes as comments. This is in sync with the standard WP functionality. However, if you have any other plugin on your site that saves custom data as comments, you may find that the WP admin panel shows extra comment counts, despite there being no extra comments. 

What happens here is that while GetPaid tries to exclude invoice notes from the total comment counts, the other plugin overrides this and excludes its own comment type instead. This results in extra comment counts being shown by WordPress. 

There is nothing that can be done to prevent this, but it should not be a problem, since your site visitors are not able to view your comment counts.