Hi Dori,
Might be, in those emails there are more than one users in the reciepient list and one of the recient (CRM User) already synchronized those items into CRM.
So when you are synchronizing, as those emails are already there in CRM so it give error: "This e-mail is already being tracked in microsoft dynamics crm".
you can look in CRM those emails should be there. Just you can ignore error messages.
Also you can verify below option in system settings, it will minimize the error messages. If email is send from one user to another user, system will create two activity one for outgoing and another for incoming.

Chandan