Suppose you have two students who have just started college. We'll call them student1 and student2. Suppose student1 takes classT, classU, classV, classW, and classX. Suppose student2 takes classT, classU, classV, classW, classX, and classY. In other words, student1 and student2 have five classes together, but student2 is taking one extra class.
Suppose that student1 gets A's in classT, classU, classV, and classW, and gets a B in classX, making his GPA a 3.8. Suppose that student2 gets A's in classT, classU, classV, classW, and classX, and gets a C in classY, making his GPA a 3.67.
Now even thought student2 didn't do that great in classY, he still had to do some work and understand some stuff in order to get a C. Otherwise, he would have gotten an F. If he hadn't taken classY, his GPA would have been a 4.0 instead of a 3.67. So in other words, student2 got a lower GPA than he would have if he had done less work, which doesn't seem right to me.
Among the five class the two students took together, student2 got a better GPA than student1. That means that student2, on average, understands the material better than student1 among the classes they took together. In addition, student2 understands some of the material in classY, whereas student1 doesn't understand any of the material in classY, since he didn't take the class. There wasn't a single class in which student1 demonstrated a better understanding than student2, but there are 2 classes in which student2 demonstrated a better understanding than student1, and yet, student1 has a higher GPA. This just doesn't seem fair to me.