Employees are generally supposed to clear after revenue passengers, unless there is some extenuating circumstance, e.g. a mechanic needs to be sent positive space to fix a plane. From what the employee said, this does sound a bit like shenanigans, since the employee wasn't expecting to get there.

Did you get on the flight? Standby can be a great benefit, and it's nice that it's free on AA/DL/UA for all revenue passengers now.