At 49'17", Celia just said "we can't tell the Austrians about Ahmed", and Ernst lifts up a file in the background; the file is down on the table in the next reverse shot when Vick answers "it's Langley's call".
When Chris Pine waits for Thandie Newton in the bar of the restaurant, his glass of wine is full when he takes his first drink. Ten seconds later, when Thandie Newton arrives, he finishes his now nearly empty glass.
The film is established as taking place on February 19, 2020. At one point Chris Pine's character looks at his phone and it says Friday, February 19. February 19, 2020 was a Wednesday.
Light shining through the "bacon" Henry feeds to Celia in the restaurant clearly exposes that it's veggie bacon, not real bacon, despite several comments about it being real bacon, including Henry calling Celia out for liking it after she claims she doesn't eat meat anymore.
In the 2012 scene outside the CIA Station in Vienna, there is a 2015+ black Chevy Tahoe parked.
By the end of the 1970s, the term stewardess had generally been replaced by the gender-neutral alternative flight attendant. Surely a CIA station chief in 2012 would be 'politically correct'.
Near the beginning of the film, Chris Pine's character drives to Carmel-by-the-Sea. But he's shown driving south on the Pacific Coast Highway over Bixby Creek Bridge, which would take him in the opposite direction.
Prior to 9/11, passenger compliance with hijackers made sense since hijackers would likely not kill the passengers unless provoked. After 9/11, the assumption among passengers and air crews are that any terrorist means to kill them. This means that any threat of violence from someone would be met with forceful resistance from passengers. In the post 9/11 world it would be impossible for four terrorists with guns to control a plane full of several dozen passengers.