I assume you mean the user is hanging up after hearing their message instead of deleting it or marking it read (saved). The default behavior for both Unity and Connection is to mark messages as new (unread) when the user hangs up without taking any action on it - this causes the notification engine to trigger on it.
You can change the behavior of the conversation to mark messages as read on hangup instead which will resolve this issue (although users should really delete messages they don't want or their inbox is going to fill up - just a side note).
I'll assume you're at Unity Connection 1.2(1) here - if that's not the case, please provide the full version/product you're running.
In CUC 1.2(1) you'll find a setting called "Mark Messages Saved If User Hangs Up" under System Settings | Advanced | Conversations. This will be unchecked by default, if you check it and select "saved" then all messages user's hang up on without taking action will be marked read (saved) instead of new (unread). Should solve your problem I think.
