After recent update I always get one topic in Unread:
... but nothing inside:
Me too ... 
Do you use more than one device to access the forum?
Unread counts are frequently wrong, but usually get corrected in a day or so as the background processes progress.
After selecting "Dismiss New" does the count re-appear?
This is very hard to debug since not everyone sees this problem. Try logging out/in as a last resort. If still not working correctly by the weekend, I will escalate the problem to the Discourse devs.
I pressed "ignore new"...
and the count is still showing as "1 unread"...
If I go to the "unread" section, there's nothing...
I've already tried logging out and back in to the forum...
I don't know what else to try...
It's not a big problem, just an annoyance...
Don't worry, the real problems are different. This can be solved even over a long period of time if you don't have the time to deal with it. 
Only one device and yes, it does reappear after dismissing it.
I am also observing ghost notifications, like counter showing 1 then clicking through and finding nothing. For the moment, I noticed this on two devices, my work laptop (Windows) and my personal desktop (Linux), both Firefox (not same version). Additionally, a full search for a keyword like "discourse" , often leads to an error 500.
I just got a notification on a thread from 2022. That thread got closed back in 2022 as well, so that doesn't compute.
As an admin, I have seen these phantom notifications in my "messages" (usually under the moderator mailbox) even though there are no new messages. I've been observing this behavior for several months, at least, and on ChromeOS (obviously Chrome Browser) as well as Mac OS + Safari and Linux + Chrome Browser.
In my case, I'll open the moderator mailbox and then reload the page. That clears the flag.
I wonder if a similar approach will fix the problem for other users (by viewing the respective area from which the phantom notification is generated, then clicking the reload button on their browser).
It didn't work.
bummer. Thanks for trying, though.
Given that this discussion is based on much more recent changes to the discourse software, I guess what I have been seeing is not directly related to the new issues.
Discourse apparently has had a history of flaky Unread/New counts. The SQL involved to determine this info for an individual is a bit complex. If I get some time in the next day or 2, I will see if I can find the topic or topics triggering this behavior.
It may also be related to some recent DDoS attacks on the forum by frequent bogus search queries which are causing worker processes to time-out. More on this later.
The issue has been fixed. At least for now.
I have again 2 unread messages in the notification but they disappear when I click 
I've got the same issue with frequently one phantom unread. It seems to be an upstream bug: https://meta.discourse.org/t/unread-count-shows-unread-14-but-unread-is-empty/403986/14
and possibly: