If you are using IBM Lotus Notes Mail and the unread message count is wrong, then it may be the ‘views’ are not built properly.
Two possible solutions:
From within the mail file, goto Edit -> Unread Marks -> Scan Unread…
It may prompt you to re-build the views, in which case say Yes.
If you are still having problems, then from within the mail file press Ctrl + Shift + F9 to force a rebuild.
Close and reopen the mail file and the problem will hopefully disappear.