We have received multiple reports of multiple notification types acting erratically. I myself have seen this happen as well. Users and moderators are reporting on Pop-ups for months old PMs they have already read and replies to, Notifications in the notification panel for posts they've already viewed, and clicking on notifications takes them to a many posts before the one they were notified about. so far those are the three "errors" I've been told about, might be there are more.

does anybody else encountered this behaviour and/or are the Devs aware of this?

Considering your other topic where plugins are randomly disappearing, I'm wondering if your database is corrupting which would explain all of these issues potentially.

I don't think those are related. the disappearing plugins thing is pretty old, while the notifications only started acting up after the 4.5.4.2 update. HOWEVER, it looks like we've figured the notifications out. Something (no idea what, I'm not the one who fixed it and not the technical authority on our website) was getting the notifications sending stuck and not completing even after hitting 100%. So the queue very quickly got to several hundred tasks and was dispatching the notifications a good few hours or days late.

The fix was applied last night and so far it's going good. But I want to let it run for a few days before being we can be sure it's good.

You may want to audit whatever modifications you've made, as the behaviors you're seeing in your community suggest something's behaving very badly.

Are these all Marketplace things or do you have custom development?

Everything is originally from he marketplace. We have done no custom development.
It does, however, seems like the issue has been cause by something that happened during the update and has been resolved.