My blog only gets spam comments and as such, I delete them (they never actually appear as I have it set up so they have to be approved). Problem is, the number of comments never gets updated against an entry, so one of my entries still claims to have 80-odd comments.
I've looked into the source code and the problem appears to be in the method called deleteComments in module_comments.php - in here, it deletes the comments from the comments table, but never updates the comment_count column on the entries table.
Hopefully you can include a fix in the next release. Though, (and this will be more work) it would be nice if the number of comments shown against an entry was the number of approved comments, as this may lead to confusion if someone sees 20 comments when PivotX reckons that there are in fact 23, for example.