After some crashes of mail.app you will finally end in some items shown in only in the client app. Obviously, this happens only when using IMAP or Exchange accounts. However, the traditional solution was to remove the account and recreate them. Since the sync depends on the size of items to synchronize, I was frustrated to wait for the complete sync and stopped cleaning these stalled items.
Finally, mail.app contains a “rebuild mailbox” options, which only rebuilds affected folders. Once you select the folder, select “rebuild mailbox” from the “mailbox” menu and sit back. A complete sync will bring you inbox up-to-date.