When Paris is showing Rory the order to unlock the locks, 9:58, she says the unlock the bottom lock twice: "you have to unlock the middle bolt first, the bottom bolt second, the top lock third, the bottom lock fourth." All four locks/bolts are dead bolts.
Lorelai tells Luke she dropped a check off to the caterer's. Sookie catered her own wedding, so it makes no sense that she wouldn't cater her best friend Lorelai's, even if the minister's sister runs a catering company.
Rory gets in her car and starts to drive away, but when a close up is shot of the side of the car it is clearly not Rory driving. A man's hairy arm with a Hawaiian shirt and gold watch is shown steering the car out of the driveway.
When Lorelai and Rory come back from Atlantic City energized, Luke asks them if they believe in jet lag. Jet lag typically happens when someone travels over multiple time zones. Atlantic City and Stars Hollow (located in Connecticut) are in the same timezone, so Lorelai and Rory would more than likely not suffer from jet lag.
When Paris is giving Rory the tour, she says they lock all the locks, even when they are home. She then puts on the chains, turn two locks, and leave the remaining three locks open.