It is possible that the NRSA handed the gate agent the standby boarding pass and in haste, she just grabbed the printed BP off the counter without realizing.
Once the standby passengers are cleared (including NRSA), and it is beyond departure time, I don't think they will take the NRSA for for SDSC passengers. Perhaps Widgets can correct, but it is my understanding once the list is clear and its time to push, its time to push.