Byer says that he found the video of the Treadstone/Outcome bosses at a party on "YouTube." The Bourne Legacy takes place concurrently with The Bourne Ultimatum, which based on date references in the previous films is set no later than February 2005. The first video was not uploaded to YouTube until April of that year.
While waiting in the airport to fly to Manila, Dr. Marta Shearing walks over to a newsstand and glances at a USA Today paper about the lab she worked at. The headline next to it read "Tablets Take PC Evolution To Next Level". This was a headline from 2011, but the events of this movie are occurring no later than early 2005.
This film is set no later than February 2005, however in the movie, the song by Rodney Atkins "Cleaning This Gun" is playing on the radio. That song was not recorded until 2006 and was not released until 2007.
To apprehend Aaron Cross and Marta Shearing, LARX #3 commandeers a parked Manila police patrol car, a Toyota Corolla. But when he swerves into a busy street, the patrol car is now a bigger Toyota Camry.
The location of Aaron Cross at the wilderness outpost as seen on the display at Drone Command is 61 48 28.54 -142 49 06.17 (or 61.632507,-142.968292), which has an altitude of 8900 feet. The aviation chart seen on the same display, which shows Aaron's tracker beacon, lists the latitude as 66°, not 61°. It also lists a Minimum Obstacle Clearance Altitude of 4600 feet (which would be underground if the drone is flying at the beacon's coordinates).
When Aaron shows up at the remote house to rescue Dr. Shearing, he finds her upstairs with an empty revolver. When he kneels down in front of her, with the camera over his shoulder looking at Dr. Shearing, he grabs the gun with his left hand. When the camera angle changes to looking at Aaron over Dr. Shearing's shoulder, he is shown grabbing the gun again.
During the pursuit of Cross and Dr. Shearing, it's mentioned in the operations room that they took American Airlines flight 167 from JFK to Manila. However, American Airlines flight 167 actually goes from JFK to Tokyo's Narita airport.
A pack of wolves are shown attacking an elk. However, the only elk in Alaska are limited to a few islands, far from Aaron's location in the Wrangell-St.Elias Park (as shown by his coordinates at Drone Command).
In the climactic car chase in Manila, LARX #3 is seen driving a Manila police patrol car, a Toyota Camry. The Camry, priced as a near-luxury car in the Philippines, has never been in the fleet of the Manila police.
In the film, Shearing and Cross take a direct flight from New York's JFK Airport to Manila via American Airlines. In real life, there are no direct nonstop flights from New York to Manila, and American Airlines does not have any flights to Manila.
When Aaron nimbly ascends the outside wall of Marta's house, the stunt man's supporting wire has been digitally removed - except for the point where it passes through his clothing, which is still visible.
The goof item below may give away important plot points.
Near the end of the movie, Noah Vosen tells the investigation "We had a problem with Treadstone six years ago," referring to the events of The Bourne Identity. But this story "The Bourne Legacy" and its companion piece The Bourne Ultimatum both begin shortly after the end of The Bourne Supremacy, which takes place only two years after "Identity." So by now it's only 2 years, plus maybe a month or two, after the "problem with Treadstone."