The rule I think most refs don't understand or choose to enforce outside of the last two mintues is the 5 second rule. When closely guarded you can't hold the ball for 5 seconds. You can't dribble (generally dribble without driving to the basket) for 5 seconds. You can't hold the ball after your dribble for 5 seconds. Penn State was given a 5 second violation after about 7 seconds and was shocked at the call.
"The closely guarded rule is in effect in frontcourt only, when a defender is within six feet of the ball handler. Up to three separate five-second counts may occur on the same ball handler, holding, dribbling, and holding. The count continues even if defenders switch. The five-second count ends when a dribbler gets his or her head and shoulders ahead of the defender."