It is possible that messages can be created with the same Message-ID. One example is via a mass mailer application. These messages are grouped by the journal archiving process and in certain instances only 1 message is removed from the journal mailbox and all other instances of the message are left in the journal mailbox. These messages will not be removed from the mailbox.
No errors are generated.
This issue has been addressed in the following release:
Enterprise Vault 10.0.4 Cumulative Hotfix 3 Release
Enterprise Vault 11.0 0 Release Details