What caused the plane crash in breaking bad season 2 final Ep ?
The implication was that the air traffic controller made a mistake. The ATC was Jane's father, and was no doubt broken up by her death. Her death was from choking on her own vomit while high on heroin. Walter was in their house at the time, and could have saved her. He chose not to. This elaborate chain of events is intended to put the blame for the crash on Walter's meth production.