Why customer replies are not threading onto the ticket
The reply arrives as a brand-new ticket instead of joining the conversation. Four causes, in order of likelihood.
The ticket reference was stripped
The outgoing template must include the ticket reference in the subject line. If a well-meaning edit removed it, threading breaks immediately. Restore it in Admin → Settings → notification templates.
The customer wrote from a different address
Add the second address to their customer record and merge the stray tickets.
The mail fetcher is reading the wrong folder
Check that it polls INBOX and that no server-side rule is filing support mail elsewhere before the fetcher sees it.
A forwarding chain rewrote the message
Some corporate forwarders rewrite headers. Point the desk directly at the mailbox rather than at a forward wherever possible.