You should post here: !lemmy_support@lemmy.ml

This is not a technical support community.

(but also i’ve had the same issue since the last lemmy update, i suppose a bug made its way in there.)

Click the envelope in the top right corner.

If you reply to the reply then they tend to go away.

If you don’t reply they tend to hang around and there isn’t an obvious way to mark them as read unless you log into Lemmy via the web, in which case you can tick them as read.

Is this about a specific app? On the web interface there’s a button “mark all replies as read”.