Continuity mistake: The amount and pattern of the golf balls on the Palmers' living room floor changes between shots.
Revealing mistake: When Leland Palmer is locked in the cell he starts screaming and runs headlong into one wall, then the other. The first wall wobbles noticeably on impact, indicating it is being shot on a set.
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.
Character mistake: At the Roadhouse Cooper states that the second victim (Maddy) was found dead two days ago. It has been less than 24 hours since the body was found: he likely means she was murdered two days ago.
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.
Continuity mistake: Nadine decides to lift leg weights beside Mike. She sets it to 600 pounds. However, whenever it changes view to her lifting from the angle of Mike, whenever the coach asks her to join the team, you can see that Nadine is not lifting any weights. (00:19:45)
Continuity mistake: When Mike Nelson asks Donna for help in dealing with Nadine, Donna's right hand is inside her locker, looking for something. It then mysteriously jumps to the top of the stack of books she has in her other hand. (00:12:45)
Continuity mistake: When James is talking to Evelyn Marsh after fixing her husband's car, Evelyn's hand jumps from her lap to the steering wheel between shots. (00:22:00)
Visible crew/equipment: When Audrey enters her father's office to find him in the middle of his Civil War recreation, a boom mic dips into the shot over their heads. (00:18:40)
Continuity mistake: When James and the blond women decide to have a cup of Champagne together, James put the bottle down on the seat and while they're discussing the bottle vanishes. (00:33:30 - 00:34:15)
Continuity mistake: When Donna confronts her mother about Ben Horne, she is asked to pass the peas. Her mother fills her plate with peas. Only a few sentences later Donna is asked again to pass the peas and her mother fills her plate again, without having eaten anything in between. (00:42:10 - 00:43:10)
Answer: The answer to pretty much any question beginning with "Has David Lynch ever explained _______?" is: no.