Update: As of Saturday J Crew sent me a statement via email saying my gift card (which was my original refund medium) had been charged for the amount of the second purchase. But my bank account showed nothing. However, as of today I have received a refund to my account.
I still feel J Crew owes me an explanation as to how my credit card was charged after I read off the gift card number to the representative and she read it back to me. I also am disappointed in how this whole situation was handled. But I have my money back and that's all that really matters.