With one account, I made a new post at https://www.mediawiki.org/wiki/Talk:Sandbox
With a second account that is watchlisting that page, I received an updated Red Badge (1), and the flyout said "Message (1)", but the item itself was not visible in the flyout.
When I close the flyout, and then re-open it again, it is displaying the "Alerts" tab. So it is somehow marking the topic as visited/read. (possibly a separate issue, or just interconnected).
(reported by Hhhippo at https://www.mediawiki.org/wiki/Topic:S7lij74qkba2lq3r )