In my case it's Caprine (Facebook messenger app). In `caprine.desktop` I added `X-GNOME-UsesNotifications=true` and `Categories=GNOME;GTK;Network;Chat;`, but I only get notifications in the notification center and bubble notifications, without a red badge like there is one in Mail or AppCenter. <br/>
This might be an answer, but I'm not sure if it still applies to Juno: https://elementaryos.stackexchange.com/questions/123/how-do-i-enable-notification-badges-on-plank