As Rachel pulls out some of Jennings' clothes from the rucksack she takes to the hotel room, you can see there is a silver photo box on the bed. After she asks if he remembers her, she then opens the rucksack again and removes the silver photo box and places it back on the bed for a second time, saying it was for him.
Jimmy's party invitation to Michael includes "P.S. THE RED SOX LOST" - clearly indicating his awareness of Michael's favorite team. Jimmy later directs his decoy Rachel, at times feeding her verbatim lines via hidden transmission, to deceive Michael. Yet when the ruse is almost complete, he lets it fall apart by neglecting to feed his decoy the answer to Michael's question, "What's my favorite baseball team?"
At the beginning of the motorcycle chase, a blue Dodge Neon can be seen forced off the road by a pursuing Lincoln. A moment later on a straight stretch of road, the same car has a close call with the same black Lincoln.
When Michael Jennings looks carefully at the Albert Einstein stamps through a magnifying glass, in one of the stamps Einstein has a squared eye, formed by six little black squares (the newspaper pages). Later, when viewing the stamps through the microscope, the eye is rounded, with six white squares inside.
As Michael runs away from the approaching train, he leaves behind the guy who just got electrocuted on the tracks. Presumably the train would run over the body, but it keeps coming unimpeded until Michael short-circuits the switch.
The ID card that Michael sends himself gets used twice in the movie - once to access the restricted area, second to access the machine. Both times the card (prop) is different from the originally shown on FBI surveillance, and other "envelope inventory" shots (the number of the card that appears first several times is 071486036043).
Right before Michael is about to use the bus pass, he runs into someone and drops his envelope. You can see behind him that he clearly drops the hairspray but when they show what he dropped, the hairspray isn't there and he never picks it up.
Near the end, when Rachel is behind the glass door and yelling at Michael for not going with her, she has blood on the front and back of her hands. The blood on her palms doesn't change much, but the blood on the back of her hand totally disappears.
During the motorcycle chase scene the tires on the motorcycle change. When they are riding through the streets, the motorcycle has slick tires. When they get to the dockyards/warehouse the tires are off-road (studded).
Fairly early in the movie, when Jennings is having lunch with Troy, he dumps out the contents of the manila envelope on the table. When the two notice that they're being watched, Jennings hastily scoops the items back into the envelope; however, we see that he misses the bullet. In the next shot, the bullet is still on the table, albeit partially obscured by a napkin. The two men flee, leaving the bullet on the table, yet somehow Jennings has and uses it later in the movie.
Supposedly set in Seattle, yet there are many clues giving away the Vancouver, BC filming location. For example: the mountain range visible in the background during the motorcycle chase sequence, and the pamphlet holder on the bus labeled "The Buzzer" (BC Transit's newsletter). Other attempts to add Seattle flavor don't quite work: during the chase through an industrial area Wolfe mentions the intersection of "Pine and 6th" (which is in the heart of downtown Seattle); an FBI agent mentions "Southgate BWM", a fictional location probably based on actual Seattle-area locations "Northgate" and "Southcenter".
The key to the BMW is that of a BMW car. It has the standard Trunk/Lock/Unlock buttons on the key. A BMW motorcycle key is quite a bit smaller with only a silver metal case at the top of the key. Further as Jennings runs around the car lot he is pushing the BMW logo in the middle of the key, this is the Lock part of the key which would not reveal the vehicle he was seeking anyway. The action of the lock part of the key on already locked BMW 3 series is to turn the interior light on. Not visible in daylight.
When footage of the nuclear explosion is shown, the mushroom cloud appears, fully formed, immediately following the flash. Mushroom clouds, which are caused by debris being sucked into the powerful vacuum created by the blast, take several seconds to form.
The "checkpoint" from where Michael's memory was supposed to be erased after finishing his first job is shown in a monitor as him walking with the box under his arm. However, he wouldn't have this image in his brain, but instead one from his own point of view.
The rear-hinged half-doors on the Honda Element will not open unless the front doors have been opened first. However, when Jennings first arrives at the bank in an Element taxicab, he is seen getting out of the cab through a rear door even though the front doors remain closed.
The newspaper clipping that falls out of the party invitation has an unlikely typo in its heading: "Nexim announces it's answer to ARC's living display". The correct possessive form of "it" is "its". "It's" is a contraction of "it is" therefore the newspaper article heading is saying "Nexim announces it is answer to ARC's living display".
The microscope Michael uses in the school is that of an inverted light microscope that uses light to shine through the image and into the eyepiece. Using this type of microscope, the image would have to be clear, such as a microscope slide, for the light to pass through. If he tried to use this microscope, the image would just be black. Secondly, the images would be upside down, so when he moves the eye of Albert Einstein down, the image on the screen would actually move up.
Although the cigarettes in Michael's envelope are "smokeless" (according to the secretary's list and the pack), one does indeed smoke when Agent Dodge lights it and blows toward the smoke detector. This is less likely a goof than a deliberate trick by Michael, who may have replaced one of the smokeless cigarettes with a regular one so that it would set off the smoke detector, despite the label on the box, thus surprising the agents.
When Michael starts his tenure at Allcom he is forced to hand over all the personal items he's carrying, including his watch, as he won't be able to take them inside with him. Three years later a watch is given back to him in the envelope as part of his paycheck. When he claims during interrogation by the FBI that none of the items are his, the watch is removed from the envelope and fastened back on his wrist to show that the tan lines match. However, the watch that was given back to him wasn't the watch he initially had. He could have been wearing it the entire time he was working on the project, up until the time he switched the items in the envelope (he would have needed a new watch, since his old one was confiscated when he entered the building).
The envelope of Jennings's belongings supposedly consists only of ordinary, harmless items that wouldn't raise Allcom's suspicions, yet somehow this highly security-conscious company lets him keep his access pass, and a bullet. As a close friend of the company owner though, he might have been subject to less scrutiny in this regard. Alternatively, he might have seen the way to pass these objects in the machine.
The film was made in 2003, yet Jennings comes home after a high-tech mind erasure after engineering a holographic computer, and inserts a very low-tech VHS recording of a Red Sox game. While seemingly an anachronism, he may simply possess a personal preference for this kind of medium, as some people still do in 2010.
Shorty cuts the power at the terminal however the Pepsi cooler's lights are still on when Jennings throws the guy into it. However, it could be attached to a different power generator, as sometimes happens in the real world.
The goof item below may give away important plot points.
The newspaper that lines the bottom of the birdcage at the end of the movie is clean. It would be certain that the birds would have covered it with dropping by that time if no one was attending to them. The lottery tickets would have been discovered if anyone was maintaining the cage.