I have the same thing. Some of our clients have email settings where it adds an "(External)" prefix to email responses that it detects are going outside their company. This creates a duplicate FreshDesk ticket.
Another variation on this:
interacting with a non-English customer, their email adds "SV:" to the email title (Icelandic for "Re:").
FreshDesk interprets this as a new ticket, and an agent needs to manually Merge them.
sloppy :(
Update in case it helps someone else in the future:
The frustration on this reached critical mass for me so I opened a ticket.
The key is that in your email template, you have designate the ticket number in a specific way so it all gets consolidated:
>#{{ticket.id}}]
Now works like a charm!
In which email are you placing this? Sorry I am still learning this but so tired of getting multiple tickets because the requester replies to the email sent.
Go to Admin \ Email Notifications \ Requester Notifications
Select each outgoing email (particularly the New Ticket Created, Agent Adds Comment to Ticket items), edit the title and ensure it follows the noted syntax.
For example, my New Ticket Created notification is "Ticket Received - {{ticket.subject}} - [#{{ticket.id}}]"
For some reason, this syntax wasn't the default, at least on my FreshDesk instance.
The point still is that the Ticket Identifier should be part of the email x-header, at least in addition to that.
https://support.happyfox.com/kb/article/297-threading-without-ticket-id-in-the-subject-line