I already had a few times the problem that emails in Apple's Mail application got messed up. This means that when you select an email in the "list" view, the email that is then shown in the detail view does not correspond to the selected list entry. Also double-clicking the email in the list view opens the wrong email, which has nothing to do with the information shown in the list view about that email (sender, subject, etc).
To fix this, you only need to rebuild Apple Mail's database. Select the mail account / folder in the mailbox list on the left. Then go to the menu "Mailbox" and select "Rebuild". This rebuild might take a while, but then the email list to email detail links will work again correctly.
I guess Mail gets mainly messed up with its indexes because of Mail.app crashes.