In a nutshell, we have here the problem with the TSA. Management (Screening Managers, AFSD's, FSD's and above) do not care to take the time to know what the procedures are.
If these people cared, there would be no problems with wrapped gifts, or passengers going through the checkpoints wearing their shoes.
As for the people who missed their flight, was it a Checkpoint Supervisor who made the decision, or a Screening Manager?