Common causes of missed selectee screenings (and resultant gate screenings):

1. Contracted ticket reader failed to properly route the selectee passenger into the appropriate lane (for those checkpoints that have a separate selectee screening lane).

2. TSA failed to properly identify the selectee (for those checkpoints where TSA screeners check boarding passes at all of the WTMDs).

3. (as pointed out by eyecue) TSA failed to properly annotate the boarding pass even though selectee screening was conducted. (Holy hell to pay for that mistake.)

4. (as pointed out by eyecue) Selectee passenger is making a connection but never left the sterile area; the gate agent isn't aware of this and either calls for a TSA gate screening or redirects the passenger to the checkpoint for selectee screening.

5. Airline employees, mostly crew members, are designated as selectees but use their airline identification to get through the checkpoint to purposely avoid the additional screening. Always end up getting screened at the gate anyway.

Also pointed out by eyecue, there are instances when passengers are issued a "security document" which is not a boarding pass but allows the passenger to process through the checkpoint. Usually, the security document will have the four SSSS if the passenger is a selectee. However, I've also seen it when the security document did not indicate selectee status yet the boarding pass, when issued at the gate, did. Don't ask me why the same computer system which spits out the security document at the ticket counter prints out SSSS at the gate.