Found in production and betalabs.
When only cross-wiki alerts are present in Alerts, mark them as read - the blank Alert flyout will be displayed.
After refreshing the page, Alerts display proper 'There are no notifications' message.
It's easy to reproduce the issue with creating a new user.
- On enwiki create a new user account.
- Sign in to another wiki and enable cross-wiki notification on that wiki.
- The new user will immediately see Alerts displaying one new notfication.
- Click to expand it and view the Alert notification from enwiki (Welcome a new user msg).
- Mark it as read - the Alerts flyout becomes blank.