at shake shack -- how did the scam work?

I'm pretty sure I saw someone steal from his employer. But I don't quite know what the angle was. Maybe if my reader has a sense, you can clue me in.

Ethan and I went to Shake Shack and ordered three sandwiches. We were using coupons, so two of the sandwiches were free. We were paying for the third. Given that, there were a few things that were odd:

• The cashier insisted on splitting the order in two -- one order consisting of the sandwich we were paying for, and one consisting of the free sandwiches.
• We got a buzzer with a number for the paid-for order -- that's normal. But for the order with free sandwiches, the cashier put it in under his own name and said he'd give it to us when it was ready.
• When processing the order with the free sandwiches, the cashier pulled a credit card out of his wallet and ran it through the reader.
• Each order came a receipt showing the full purchase price.

I assume this had something to do withe processing the free order as if it was being paid for, and then processing a refund through his own credit card. But we didn't pay for that order, and I don;t understand how he was able to process a refund for something that was never paid for in the first place?