I used the clear all unreads shortcut (shift + esc) and it doesn’t go away…
Edit: For anyone having this problem, I’m using GNOME desktop environment and clearing the notifications on the shell removes the bubble on the app icon. Thanks to @EmasXP for the hint.
I think this happens when there’s notifications from Slack in the notification center. For some reason it does not seem to sync. Clearing in the notification center is probably going to “fix” the badge counter
Clearing my notifications on GNOME actually worked? You’re right, it doesn’t sync to the notification center.