When you receive a new ticket notification, all of the agents on the product are on the To: field of the email. I think this is a problem, and here's why.
When an agent hits reply, the email is sent back to the alias on the Freshdesk queue, which results in Freshdesk sending out an update on the ticket, again, to all agents. This is normal and expected behavior.
If the agents chooses reply to all, the email will go to 1) Freshdesk (just as above) but also 2) a second copy would go all the people who were originally notified -- ergo, a duplicate email situation (that second copy is "just an email", i.e. it's outside the Freshdesk system).
In contrast, the way RequestTracker works, is that it sends one email to each recipient -- thereby eliminating the reply vs. reply to all situation; replies can only go back to the ticketing system, which, in turn, then notifies everyone else.
Clearly the best practice here is to always use reply, and never reply to all, however I think this should be enforced the way RT does it.