Two interesting rules that I have seen discrepancies in....
#1. Hand ball. It is the age old question of whether it was ball to hand (inadvertant) or hand to ball (intentional). Also, if an unintentional hand ball leads to an advantage for either team.... Different high school refs call this foul very differently.
#2. Throw ins. In high school, it is my understanding that ANY foul throw results in a change of possession. This includes things such as not bringing the ball back far enough, spinning the ball, taking the throw from the wrong spot, picking your foot up, etc. The main one is that throws that never come in bounds are now a change of possession. However, in some scrimmages, I have seen this rule incorrectly applied.