The original test marking sheet was designed by an RTITB manager in 1974 and, although there have been a number of changes to the test, the penalty faults and scores have generally remained the same.
I have always advised that if a trainee does something that you think should be a fault but is not on the marking sheet, you note it and have a discussion with the trainee afterwards to make him aware of your concern and to put him right, but you cannot penalise him. Alternatively, if it is serious enough, you can always disqualify his test and make him retake it.