If you are sure that you ticked the extra box, then you most likely did, and this could just be an instance of stress caused by the HSC exam period, which is perfectly normal to experience. Perhaps you should not worry too much about it
On the other hand, it may be difficult to tell the outcome of not ticking the box, i.e. whether the extra papers you have used will be marked or ignored because I don't believe markers adopt a strict and merciless approach in that regard. I believe they would be considerate of the fact that stress may lead to such incidents and will consequently do their best to ensure that the student is not disadvantaged. However, this doesn't mean that not ticking the box does not put the student at risk in the first place, which is an important thing to keep in mind with respect to your remaining HSC exams going forward.
I hope this helps!