Chloe informs Jack that the co-pilot of the flight, Scott Evans, is working for Henderson. When Jack relays this information to the pilot, he mentions the name of the usual co-pilot, Don Faginson, despite the fact that Chloe never said it to him.
When Karen Hayes sends Chloe the flight information for the diplomatic flight, she says that it is "Flight 520 to Frankfurt", but the flight plan she sends to Chloe's computer shows the destination as London Heathrow Airport. Additionally, the flight plan shows a departure time of 2000 Zulu, which would be 1:00pm in LA, despite the fact that it is actually taking off after 2am. Finally, the planned speed is listed as 620 knots which would be supersonic and well beyond any speed a Boeing 727 could reach.
Jack and Chloe wouldn't have been able to contact each other through their cell phones while he's on the plane because there would be no signal.
At approximately 2:36 a.m., as Jack places his cell phone down on the floor of the cargo hold, there's a close-up of its display that lists the time as 8:04 p.m.
At 2:30 a.m. when Mike is entering Martha's Room, a crew member in black is visible in the hallway behind Mike, on the right.