Due to complexity in the Exchange systems and networking it is often due to subtle misconfigurations or lack of proper preparation for mail migration. There can be many reasons causing mail to go missing. For example,
1. Throttling in the target or source environments can slow migrations down giving the appearance of missing mail.
2. Mailbox corruption can leave messages ignored and passed by.
3. Mailboxes may be locked by other utilities and therefore bypassed or stalled.
4. Antivirus systems for the Exchange servers may be causing issues.
5. Even unknown occurances that leave no trace of an error may prevent mail from being migrated.
Perform a full "resync" on the mailbox or mailboxes(s).