Are you able to provide more details on how the new deal is being created? Is it being done manually from the contact record? If so, there are some checkboxes at the bottom of the deal creation form that may be causing this association. If the company timeline is checked, all the previous emails are the company record they will transfer to the new deal.
Let me know if that helps! If not, providing any screenshots or descriptions of your deal creation process would be helpful for further troubleshooting!