I have a news site set up with nested comments enabled. When a comment is marked as spam it is correctly removed from the article page however so to are any replies to that comment.

This makes sense as the replies are now orphaned and don't have a parent so potentially wouldn't make any sense.

The issue I'm having though is the total count of comments still includes those orphaned comments. So an article may say it has 10 comments but actually only 5 show as the other 5 are replies to a removed comment.

Is this a bug/known issue in Wordpress as the theme i use just uses the standard wo comments system?

What would be the best solution to this, creating my own comments methods?