I've had this happen for people I've blocked. Have you tried using the "Mark all as read" button? That has worked for me before.
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Unfortunately its still an issue. I've unblocked all people to see if any message pops up. There is no Mark all as read-button. And I usually mark each single reply as read once I open it. The 2 at the notification bell icon on top does not go away, it's basically the new 0 for me. Here is a bug report from someone else: https://github.com/LemmyNet/lemmy-ui/issues/1300
Weird. Yeah, sorry, no clue past the standard clear cache/data, refresh, try different browser