I've had this happen. It has something to do with the boarding pass printing. I checked in via my phone and saved my boarding pass to my phone with a TSA PreCheck marker. I reprinted my boarding pass at the airport and the TSA PreCheck marker was missing.
Luckily I still had my boarding pass via my phone and used it. I think it is a programming issue with the boarding pass being printed at the AA's kiosk and nothing to do with TSA.