Email reply, with ticket number in subject, creating new ticket

I've searched the blog for this issue, have found a few close to the same description, but not exactly.

This is our scenario sometimes [It does not always happens this way] -
   The good -
     We have a ticket that we send out an Email message from within, so it has the ticket number in the Email.
   User replies back, also with the ticket number in the Email.
The bad -
     Instead of including this reply in the original ticket, a new one is created, but it also has the same ticket number.
     So depending on how much back-and-forth communication happens, we can get several 'tickets' with the same
       number that are not linked.

Any suggestions on how to stop this?