In a large class, there is usually a longer period of disruption at the beginning of the class because more people come in late.
Large classes are noisier, so it is more difficult to hear what's going on.
Large classes have less class discussion because students are usually less willing to ask questions in large classes. The larger the class, the longer it takes the professor to grade the homework and to hand it back during class, so there is less time spent productively for lecture and discussion. Most students don't like to be crowded together too tightly, packed like sardines in a can. The Fire Marshall says it's a fire hazard to have people sitting on the floor, exceeding the size rating of the room. Students who sit on the floor during an exam tend to not do well.