In the final scene when Nathan turns to Karen, the agent behind her touches his ear piece, turns and opens the door of the SUV to get in. You hear the door shut, then two seconds later the agent is standing at attention facing the couple again behind Dr. Bennett.
Nathan never wears a helmet while riding his motorcycle, even though Pennsylvania Law requires that any person who operates or rides a motorcycle must wear protective headgear unless he or she is 21 years of age or older.
Nathan and Karen are told to go to 3411 Clarendon Boulevard Apt#2, but actually end up going to Clarendon Avenue Apt 202 (the street and apt # are both wrong, but actually turns out to be the right place).
When Nathan confronts his mother/keeper with his findings of his childhood photos, daylight can be seen outside his bedroom window. When his mother goes downstairs crying it is pitch-black outside. When Nathan is chased and jumps out of his bedroom window it is also dark.
At the end of the movie it is stated that Nathan is in his final year of high school, making him approximately 18. Assuming the movie is set in 2011, his mother was killed in 1995, making him 2 at the time he witnessed her murder. Yet earlier on it was revealed that a photo of him when he was 5 was doctored to edit his biological parents out of the picture.
At about 1 hour into the movie, when fake IDs are handed to Nathan, their shadows (outdoors) are more than 10 feet long. In the the next shots, the hardly visible shadows are about a foot long, revealing that the shots were taken at different times of a day.
Some 54 minutes into the movie, when Nathan and the girl arrive at the "waiting location", Nathan picks up stuff from the desk. He places a gun beside rolls of euros and dollars on the desk, with his right hand and the barrel facing him; however, in the next shot, you can see a totally different position of these objects - the gun is on the other side of the table, the roll of euros is not laid down, the album disappears, the black object and the USB stick are in different places and a red die appears.
In the diner when the camera flips back and forth with the dialogue, sometimes the big red cups say "Coca-Cola" and sometimes they don't, and sometimes one cup has a straw, and sometimes they both have straws.
When Karen is walking back from the buffet car with the food and drink she's grabbed by one of Kozlow's henchman, and drops all the items onto the floor. Yet when Nathan walks along the same aisle a short period after, there is no sign of the spilled items.
The final scene when Karen, Nate and DR.Bennet are speaking in the parking lot with the agent standing outside of the SUV, the Suburban SUV changes. You can tell this by noticing the tint is different on the back windows. The other dead give way, is the type of truck wheels changes. A different vehicle was parked during the shots after the Doctor has appeared and while talking to Nate and Karen.
After the house explodes and Nathan is headed to the hospital, he is on the 7th Street Bridge. He would have passed the hospital that is on the North Shore, less than a mile from PNC park, which can be seen in the background of the shot.
In the finale, you see Taylor sitting next to the villain with a gun taped to the bottom of the chair as if he had planted it before hand. In PNC stadium the seats (in the section they were in) flip up when not being used. The gun would have been in plain sight before Taylor sat down.
In an early scene, Nathan and Karen are studying after school. She leaves to catch her uncle's phone call at home (just across the street). Before she leaves they decide to meet at her place in an hour. At the time she leaves daylight can be seen outside. When they reconvene it is dark outside. Knowing that it never stays light out in Pennsylvania past 9:00pm during the year, we can assume it is no later than 10:00pm. In the same scene, there is a cut to a guy in New York who sees Nathan on webcam and calls his boss in London. However, when the film cuts to London it is daytime. London is no more than 6 hours ahead of Pennsylvania. Technically, it should have been around 3am.
Protective headgear is required to be worn in high school wrestling in Pennsylvania (and in most of the United States), yet none of the wrestlers wear any. (Further, there are usually rules for wearing singlets in competition rather than t-shirts with sleeves ripped off and baggy running shorts, as loose clothing can ensnare and twist fingers.)
High school wrestling seasons run regularly from the start of December through February (with State competition running through to mid-March). Professional baseball seasons runs from April through October. At no point do these seasons overlap, yet Nathan is wrestling during the regular wrestling season then going to a professional baseball game a few days later.
When the CIA agent presents the Kozlow case, on the right side of the LCD you can see "known associates". The man in focus seems to have the newest Croatian biometric passport. However, the picture on it would not have been accepted as a passport photo due to dark background. Also, the picture, obviously taken from the "passport" is not edited (in Croatian passports, photos are "digitally enhanced" to emphasize ears, nose, eyes, all facial hair and the chin. As a consequence, the photos in Croatian passports look more like drawings than real photographs.
Karen has to be hospitalized for an injury to her upper arm that has to have stitches and a patch, yet, less than 24 hours later, as they sit in the baseball park after the game, she clearly has no stitches, patch or even a bruise to either arm.
When Nathan and Kazlow meet at the stadium, Nathan has a gun taped to the bottom of the seat, yet, before sitting in them, the seats visibly show what's beneath them. How can there be a gun taped to the bottom of the seat that clearly makes it visible to the public before sitting?