I kept getting the reply count ball on this thread even though I'd checked it out several times. I finally guessed that the problem was that I had not looked at a post by a user I've blocked/ignored. After opening the hidden reply the ball notification disappeared.
So, I need to view a post by a blocked user (whose posts by definition I obviously don't want to see) to close the notification.
Can you send me a video via PM if it happens again? Also, open the browser's developer console with F12 to check if any specific errors are being reported.
Currently, I'm unable to replicate the issue on my test site. If an ignored user responds to one of my posts or a tracked topic, I see the bubble on the topic list and at most the banner "See X updated or new topic(s)". However, when I enter the topic and then exit, the bubble disappears even without reading the hidden replies from ignored users.
If it happens again, before clearing the bubble by opening the hidden reply, try opening an incognito window with browser extensions disabled, log in, and check if the problem still occurs that way.
Generally in incognito mode the extensions are disabled by default. If you've never used it, you certainly won't have changed the behavior of the extensions either