We had this kind of problems - was related to mail created by users with closed mailbox.


Example:
1. User1 (his mailbox is closed) sends e-mail from SalesOrder
Since the mailbox is closed, the e-mail is created, but will not actually be saved, but PDF is created and SalesOrder gets the link to e-mail.

2. User2 (his mailbox is open) sends e-mail from Invoice.
This e-mail is saved and has SalesOrder and Invoice as attachments + links to both records (SO+Invoice) since they are related to the same e-mail number.

Was solved with HAL - did't allow sending e-mails if the mailbox is closed.