Moved items inside the mailbox are being re-archived creating duplicates in the archive.

Error Message:

None

Workaroud 1:

Items can be moved within Enterprise Vault Search (EVS). Moving items within search updates the the item's location in the index

Workaroud 2:

Use  Enterprise Vault Policy Manager (EVPM) to disable archiving on the destination folder if possible, i.e if the item was archived in folder "\FolderA" and being moved to "\FolderB". placing a DoNotArchive tag on "\FolderB" will prevent EV from considering the item for archiving. Moved items will not be updated in the index .

Refer to Utilities Guide EVPM Section for more details. 

Items were archived without creating shortcuts, when the item moves inside the mailbox it changes the modified date of the item causing Enterprise vault to archive the item again.

This is an expected behavior since shortcuts are not being used, moving the item changes the modified date and causes Enterprise Vault to re-archive the item.