Yes, first I'd try to submit your missing trip request online with the ticket number/call AGR with the ticket number. Since your ticket wasn't collected, there is no way it will post automatically. I'd leave out that detail that the ticket wasn't collected.

rafster is right in that you could exchange your ticket for a new ticket--but I'd only do that if I couldn't get AGR to post the trip. You bought a ticket and you did ride the train, so you have a right to claim the points. Seeing as you bought this ticket just for a point run, I don't think a refund and repurchase is really what you're looking for.