When Jedburgh is visiting Craven and having a whiskey, he takes a pill and clearly drinks only about a half of his drink. After this he immediately stands up and puts his glass on the table. However his glass is strangely empty.
When Craven is sick at the sink, the microwave in the background is in the corner of the counter with a yellow bowl on top of it. A few shots later when Craven is back at the sink, the microwave is about 5 feet from the corner with the yellow bowl to its right.
In the kitchen when Craven pours himself and Jedburgh a shot of whiskey, Craven puts the bottle down and the level is just below the neck. However when Craven sits back down the level drops to the "shoulders" of the bottle before rising again to the neck 5 seconds later.
When Craven is traveling to Union Street in Northampton, he is seen turning right off of Market Street onto Bridge Street. This is in fact the wrong direction. Union Street is off of Market Street, two blocks back.
e is traveling in the wrong direction.
When Craven is following Bennett into Boston's Central Artery Tunnel the scene show them getting off at exit 24, Government Center, which exits to Faneuil Hall. The next scene however show Craven pulling Bennett's car over on Rutherford Avenue which is North of Boston.
When Craven is talking to his daughter's friend in the car, when she gives him the disc, you hear a bird call. It is the sound a Western Scrub Jay makes. There aren't any Western Scrub Jays in Massachusetts. There's also another point in the movie where you hear a Western Scrub Jay, a scene that also occurs in Massachusetts. I'm guessing the movie was sound edited in California, where Western Scrub Jays are common.
When Craven intentionally backs into his two pursuers in the SUV he is on Washington street between West Dartmouth and Union park - directly in front of the Boston Cathedral. But on the subsequent news report, the incident is reported as taking place on Arlington Street.
When Tom Craven questions Burnham about the gun he loaned to Emma, Gibson says the gun is licensed in Vermont, and therefore illegal in Massachusetts. Aside from federal requirements, Vermont does not have firearm licensing or registration. Tom Craven couldn't have accessed a Vermont firearms database; it doesn't exist.
When Craven goes to Identify his daughter's body, there is no visible evidence of autopsy (assume it was done because the coroner rattles off causes of death). Being the victim of a shotgun wound to the torso, she would have had a standard Y-incision, the top part of which should be visible on her exposed upper chest.
Tom Craven says his daughter was poisoned with thallium, which he finds using a Geiger counter. While normal non-radioactive thallium causes heavy metal poisoning but not radiation sickness, there are radioactive forms of thallium which are normal byproducts of nuclear decay. The radioactive form would be more likely available from a nuclear facility than the non-radioactive form.
In the scene where Craven is driving in the rain, right before he enters the tunnel, the Berkeley Building in behind him - with a steady blue light. The Berkeley Building is topped by a weather beacon, with different patterns: Steady blue, clear view.
Flashing blue, clouds due.
Steady red, rain ahead.
Flashing red, snow.
If it was really raining, the light pattern would have been a steady Red, instead of Blue in the movie.
The goof items below may give away important plot points.
At the moment she gets out of Craven's car, Melissa is immediately struck by a car traveling at very high speed. Assuming the driver was some distance away and waiting for her to get out, it would have been virtually impossible, with only a couple of seconds notice, to accelerate fast enough to get to that spot at precisely the right moment to hit her.
When Melissa gets out of the car after her conversation with Thomas Craven, she immediately gets hit by a car which also tears off the car door. The car makes a U-turn to come back for Thomas Craven. At first glance, the front of the car seems to be completely undamaged, without a single scratch. However, closer inspection reveals a large dent in the upper part of the left fender, possibly indicative of where both cars made contact.
When Emma Craven is shot in the chest by a shotgun blast, she goes flying back a good distance. According to Discovery Channel's MythBusters, and Newton's third law, the victim of the blast would be thrown back no further than the shooter was knocked back by firing.