I'm using a new Samsung Galaxy S21, and I have this problem. First was the GitHub app that showed this red counter next to the app icon. I did not go away, whatever I did. I don't have any pending not read notifications. I open the app and click on notifications that I have turned off. And suddenly, after a few hours, it disappeared. Not sure what I did.
Now I have the same issue with the Keybase app, inPost (Polish parcel), and my Bank app (ING) it shows (3) next to the grouped app, and three of the apps inside have red (1) next to their icon.
What should I do to make them go away? Looks like a bug to me.
EDIT: I've just paid with BLIK (Polish payment system) with my bank and got 2 more notifications now I have 3 notifications from my bank and 5 for the group, that don't go away.
