My agents use Microsoft Outlook. Sometimes when they reply in a ticket, their response pulls the entire email chain into their direct response.
The reason why some responses from your agents pull the entire email chain in their most recent update is due to the default behavior of their mail provider. Outlook includes by default the original message text when a user replies or forwards their message.
To solve this issue, have your agents change the appearance of the original message to Do not include the original message. Have your agents follow the instructions described in this article from Microsoft Support: Change how the original message appears in replies and forwards.
For more information on other common email issues, see the article: Common email channel problems