Plot hole: More than 24 hours after Ben is arrested his daughter Audrey comes and asks Cooper if her father was arrested. How has she not noticed that he is absent and in jail?
Plot hole: In the bait and switch section, why does anyone involved agree to Leland being Ben's attorney when both victims are relatives of Leland? Neither Ben nor any of the police are in on Cooper's plan, and it seems implausible at best that they would agree to this.
Plot hole: Harry states that Ben was not arrested until after midnight. However in episode 2.7, the arrest takes place earlier in the evening, shown in establishing shots and the other events which occur afterwards.
Answer: The answer to pretty much any question beginning with "Has David Lynch ever explained _______?" is: no.