This articles discusses the Salesforce known issue with the <unknown> duplicates values on record with id error.
This is a long standing Salesforce Known Issue and is documented here. This is scheduled for a fix in Winter '19. In short, this error happens because of history tracking on your fields.
The easiest workaround is to turn off history tracking on your source, take a snapshot, migrate all necessary fields and then turn on history on both source and destination. This might not always be possible.
The other workaround is to create a snapshot with Store Reference to Data (see Tips and Tricks) and then editing the snapshot to remove historytracking elements in your fields. This is an advanced technique and not recommended if you are familiar with XML and Metadata API.
The Support team is always available if you need more help with getting around this error. Contact us.