Based on your wording in the email, I would refund the difference. What you do is your business.
For anyone else reading this, here's your lesson for the day. Never mention numbers of pallets or measurements unless the customer brings it up. Quote the price for the completed work. Offer no more information than you need to.
Edit: Personally I think Michael refunded the money based on the title of the thread. I don't think he would have ever brought it up if he didn't