You can't compare what is being done with referees in the NBA and the NCAA.
Much easier to deal with the refereeing in the NBA. What, there are 30 teams? No more than 15 NBA games on any given day. Total pool of 60-70 referees required to manage the games played in the NBA. That means 60-70 referees that they have to train up and get calling plays the same way.
Now compare that to the NCAA and the number of referees that it is working with. I think there are 65 P5 schools alone. That means as many as 32 P5 level college games going on at any given time and that doesn't include the Big East, A-10, AAC and other non P5, mid level and mid major conferences. How many referees are you talking about when you consider how many games are going on at any given time? Much bigger problem finding quality referees to do all those games, training them to call plays the same way etc.