First, I want to confirm with you: whether all migrated mailboxes have this phenomenon? Whether this phenomenon occurs on all old emails?
You can use “Get-MessageTrace” and “Get-MessageTrackingLog” command to check from Exchange online and Exchange on-premises. We will know when and how the email was generated:
Get-MessageTrackingLog -Sender "MicrosoftExchange329e71ec88ae*******@domain.com" -Recipients "user@domain.com" -MessageSubject "Delivered: Test1234" | select EventID,source,Timestamp
If there exist record about this email, it means email was processed twice, I would confirm with you whether there exist email filter tool in your organization which may cause this phenomenon.
If there doesn't exist related record, I think there may exist something wrong with the mailboxes, try to migrate mailbox to another database(It could repair some issue for mailbox) before migrating it to Exchange online.
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