I think his test was split (?), hence the three main questions. If you think he failed nine questions but passed three, we could always ask Mullins? Mitchell's or his mum's test also mentioned three questions.
I'm no expert on this but I think the way it's done is that there are 3 pertinent questions (what they term the 'relevant' questions) interspersed among a load of 'control' questions. The control questions are ones to which you would expect a truthful answer (or the tester knows what the truthful answer would be), and so they then compare the results to see if there was a significantly different response to the 'relevant' questions. The report is then based on the results for the relevant questions.
All of the 12 questions seem relevant to me, so if the test was actually 4 tests (as per JBs comment in the Mirror article), what were the results of the other 3 tests? If it was all one test, why does Mullins not consider the other 9 questions as relevant?