Observed in 1.29.0-wmf.3 and 1.29.0-wmf.4
There is a correlation (suggested by @Catrope) between the number of wikis from which notifications are displayed and the frequency of the issue - the more wikis are present in the Notification panel, the more likely the bug will be present.
- Login as a user who has cross-wiki unseen notifications.
- Open the notification panel and click on the blue dot to mark all cross-wiki notificaitons as read.
- The counter will still display 1 (no, it's not the case when there are more than 25 unseen notifications).
In the screen recording, the number of Alerts is 9. Upon opening the Notification panel correctly displays 9 alerts from different wikis. Clicking on the blue dot, incorrectly reduces the counter number to 1.
Note: For some reason, the issue is easier to reproduce in production than in betalabs.