When you say "returning to", how do you return from wiki B to wiki A? And once you are on wiki A, does reloading the page make the issue go away?

If your answers are "I use the back button" and "yes", then you should know that because of the unhelpful way the back button's behavior is specified, we cannot prevent alerts from still being visible when you go back: browsers are required to display a cached page, and we have no way to tell them not to.

Re-checked with testwiki and enwiki (both mobile and desktop) - it seems that 'Mark as read' functionality works as expected. As @Catrope pointed out, displaying cached versions is misleading sometime.

In T153629#2886900, @Catrope wrote:

When you say "returning to", how do you return from wiki B to wiki A?

Back button, then reload.

And once you are on wiki A, does reloading the page make the issue go away?

No, and it appears in new windows as well. I first saw this about a month ago, and the notification has stuck around until now (it only disappeared yesterday when I tested it on desktop).

The notification was created on mediawikiwiki, and observed on huwiki. I can reproduce it with a different account, but not with a different wiki (B can be anything, A must be mediawikiwiki it seems).

Hmm, I wonder if perhaps the ?markasread=NNN parameter is not processed on mobile page views? Let me test that theory.

In T153629#2887955, @Catrope wrote:

Hmm, I wonder if perhaps the ?markasread=NNN parameter is not processed on mobile page views? Let me test that theory.

No, that's not it.

Also, let me clarify the reproduction steps, because they don't make sense as written: the notification originates on wiki B, right? Otherwise you wouldn't be taken from wiki A to wiki B.

These are the exact steps I took:

1. edit User_talk:Tgr_(WMF) with TgrTest
2. open https://hu.m.wikipedia.org/ in Chrome/Android
3. log in as Tgr_(WMF)
4. click on notification menu, click on notification
5. (mw.org loads, there is no local notification)
6. go back, reload page (or I can open it directly, or even open a third wiki, makes no difference), there is still an unread notification

When using meta instead of mediawiki.org, everything works as expected.

When you are taken to mw.org, are you logged in as Tgr (WMF) there, or as TgrTest?

Probably caused by T108201: CentralAuth autologin broken for non-www mobile domains (mediawiki.org, wikidata.org).

For completeness: the ?markasread=NNN parameter only works when you are logged in as the correct user on the target wiki. Otherwise you'd be able to mark arbitrary notifications owned by other users as read. (Also, NNN is the event ID, and you need event ID + user ID to uniquely identify a notification.)