Unread marks not updating reliably in Mac Mail with Exchange server after upgrade to Yosemite

Same issue, and on two different machines. One is a MBP (mid 2010) the other is an iMac (early 2013). I am getting mail from an Exchange server. I find that closing and reopening mail will temporarily solve the problem. I also find that switching mailboxes and switching back works.

Had the same issue, and for me it helped rebuilding the inbox.

Select the Inbox then go to the Mailbox menu and then select Rebuild in the bottom of the menu.

If the option Rebuild are disabled, make sure you are in Mailbox view so you can have the folder selected. To get the Mailbox view click Mailboxes in the Favorites bar, or choose View > Show Mailbox List

The inbox might go blank/white for a while when mail.app are rebuilding its indexes. It will fetch all the emails from the server again so it might take some time for large mailboxes.