As these bills are just beginning to show up in circulation, I'm sure businesses haven't yet implemented best practices to combat this issue.

The salesperson probably took it to the manager or bookkeeper in the back area (one person usually handles all transactions) and that is when it was discovered. I'm sure they are learning to handle cash (especially $100's) differently now, and in front of the customer. It is your misfortune to have still been waiting for the piece....otherwise it would've been "one and done"....you'd be gone.