I've seen this as well. What worked for me is to click on the envelope icon at the top right and then click on the message in the Inbox on the left. This seems to clear the notification alert.
The "bell" icon just denotes recent notifications but isn't exactly synchronous. It acts more as a running count of all recent notifications and the only way to clear it is to click on it.
We'll ask our vendor if it can be customized, though 🙂
