DarkTexas
The headers of the email that created the new Ticket, and any mail that's in the original Ticket. You basically need to look at the headers for the new Ticket email, copy the In-Reply-To and References header values, look at the original Ticket's email headers (for any email in that Ticket), and try to see if any of the In-Reply-To and References header values you copied are in the original Ticket emails.
For example, let's say the In-Reply-To of the new Ticket is <123abc@outlook.com>
you need to search for <123abc@outlook.com>
in all the emails in the original Ticket.
You should also run a test yourself to see if when you reply to the emails if it goes back or creates a new Ticket that way you can better test. If you cannot replicate then you know the User isn't replying as they should. They are likely copying the original email and forwarding or something and the headers are not matching up the way they should. As long as they reply directly to the Agent replies or any alert from the Ticket it should go right in the original Ticket.
Cheers.