One of the more common problems, especially with new users to RT is the infamous "Permission Denied" email. Here are some common causes and solutions
Reply email different than initial request email
RT auto-creates an account when a new ticket is created. That user is then the "Requestor" of the ticket. If the user replies from a different email address, RT treats it as a new user, which by default doesn't have the ability to view or modify the first ticket.
- Educate user to use a consistant email
- Add the second user as a "requestor" to the ticket ("people" ticket tab)
- Change queue rights to allow the Everyone group the ability to Reply.
Queue doesn't allow requestor to post
When a queue is created, no rights are granted. You need to grant the "requestor" group the "reply to ticket" right.
Check the log
RT logs to syslog ( typically /var/log/messages, check /etc/syslog.conf for info). That may contain additional clues to pursue.