This would suggest that the users CRM user profile is not linked to the email address that they are using to send email from. 


Hence the email is being sent out to the contact but the email is being logged back inside the contact record for the CRM user instead of the contact record of the person they are emailing. 


Please check if the CRM user has a duplicate contact record?  Just type their name into the search bar to see if there is a duplicate contact record with their senders email address logged?   


If so you will need to merge the contact records together - please click here to see how. 


We will need to make sure that their CRM user profile is linked to all the email addresses they use to send email from.  


If you can please contact our Support Helpdesk and let us know the email addresses the user sends email from so that we can make sure these are added to their 'master' record which is associated with their CRM user profile.