The issue seems to be limited only to notification messages that come for any updates on User talk pages.
1. Login as user **A** who has a wikitext User talk page; go to the User talk page and stay on the page.
2. In a different browser , login as user **B ** and go to user **A** talk page to leave a message.
3. For user **A** refresh his User talk page - the counter for Message notifications will display the count of updates(on a blue background) that user **B** has done.
4. Click on the Message notification icon - the overlay will be displayed, and the counter will change to '0' but it'd be displayed on a blue background.