Factual error: The 'game' set up by Soneji is a whole bunch of computer science-fiction nonsense seen only in movies, with the common factual error of blurry pictures that can somehow be zoomed in ad libitum. The IT agent comments when Cross has clicked on a picture from the camera recording of the class; "Dr. Cross isn't in cyberspace anymore! You're at a live site, looking through a video camera", which does not even make sense. The sequence that follows is not a camera feed, with a real camera being moved, but a panoramic composite shot of the room.
Plot hole: The kids in Soneji's class use an encrypted GIF algorithm to pass notes to each other and that "drives the teachers crazy", since they are unable to catch cheaters that way. But how do they do that? Easy, they have a message system in place installed on their workstations, that warns them with a big pop-up that they've got "A new message"! It would be easy to sanction and prevent the cheating by simply removing the chat application, no matter if they use it to chat directly or pass Michael Jordan photos as shown in the movie, which they have no business doing during an assignment anyway.
Plot hole: With over two years spent teaching at school, nobody (students, coworkers) ever noticed the rubber face and rubber hands of 'professor Soneji' - and he teaches computer science, having to get close to people constantly looking at their screens and interacting with them - as shown in the classroom scene. Nothing is also said about the name being an alias and how he managed to teach to the super-elite school where daughters of senators and the Russian President (what is he doing attending middle school in the US anyway?) with no credential, or fake ones (the degree shown is in Mercusio's name). You'd think the vetting for the staff there would be iron-proof. He has also been wearing a fake gut, and something like that would have easily showed up if he ever got as much as a pat-down, which at a place with security so tight, is certainly a possibility.
Plot hole: Jezzie has files about Dimitri in her computer and is the one who asks Cross to do the stake-out at the embassy. She knows of Soneji's plan to kidnap the Russian kid, but wants it to fail, since she is more than content with the millions of ransom for Megan. This part does not make sense on any level; she can't know on which day Soneji is attempting the kidnapping, and since she and her accomplice know where he is hiding (or else they wouldn't be able to grab Megan from him when he is away), by all means they should have killed him rather than run the huge risk to let him try to kidnap another kid at the well guarded embassy and have him killed or worse, captured, before they can do their scheme replacing him. For their plan to succeed, Soneji needs to be dead, so he won't mess up for his delusions of grandeur.
Plot hole: Cross says that the best strategy to keep the kid alive is to pamper Soneji, stroke his ego and make him a living legend as he wants to be. What Soneji did though, was guide them to his real identity and name, since Soneji is just a front he used to be employed at Cathedral School, and in the first conversation with Cross he said about the Soneji name "That'll do for now." It's obvious to anyone then that he wants his real name and self to emerge from obscurity and drop the alias, and if Cross really wanted to please the kidnapper, he should have used his real name, Jonathan Mercusio. Despite these clear elements, that name is never used or referenced in the movie again.
Factual error: When Alex shoots Jessie in the chest, the blood is pouring out of the hole in the trench coat. Gravity would be doing that between her skin and red sweater instead. (01:35:15)
Plot hole: From a logistic and tactical point of view, the whole police/FBI operation revolving around the diamonds does not make any sense. The agents are supposedly spread around and in great numbers, but everyone is simply chasing him, while Cross is speaking freely through the radio and shares the addresses and instructions so they should be -ahead - of him, they know where he is going! Although, during the action, Cross tends to speaks directly with Jezzie all the time, as if all the other dozens of agents did not exist. Jezzie's presence itself is completely illogical, too, since Soneji ordered that nobody would follow Cross or he will kill the girl, and Jezzie is the one agent that he knows (she's been the kid's bodyguard for 2 years!) and is sure to recognize. She should be nowhere near the chase, but nobody objects at all.
Revealing mistake: Cross is between the first two steps of his tour de force following the instructions for the diamond delivery. McArthur says "Unit six, take "K" Street and double back", and we are shown Jezzie in her vehicle. She moves cutting through a traffic island with a forbidden maneuver, and yet you can see on the asphalt wet marks of 'someone' doing the exact same thing before her recently (obvious residual of the previous take). (01:06:30)
Continuity mistake: Cross just boarded the train. At the entrance, featured prominently, there's a woman with headphones. To the other side, there's an old pudgy man with a beret, and a black guy in a dark brown suit, looking all serious. Morgan Freeman is between these two guys, but in the POV that follows they are both on the same side, in front of him. (01:09:25)
Continuity mistake: Dimitri calls Jezzie from the gates of the embassy, and she leaves Cross and the guy talking in Russian to go to him. During the transition, the soldier moving across the gates walks through the same steps he already walked, and the bodyguard in a trenchcoat is in a different position. (00:59:25)
Other mistake: Megan is kidnapped during the lunch break, and when Cross reaches the Rose residence, his friend from the FBI tells him about the forensics exams not netting any results. When he gets to the crime scene the day after, though, it's swarming with feds who are still doing things like checking the computer stations and even photographing the chalklines of the strangled woman, all sort of investigations that you'd expect to have happened already in the previous 24 hours or so.
Continuity mistake: Cross and Jezzie are en route for Soneji's office but get stopped by a backhanded comment by agent Ben Devine. During the sequence, there are 3 people talking behind the two investigators; they are either on the left or the right side of the corridor, depending on the camera angle. They just want to be in frame. (00:32:45)
Continuity mistake: After the scene with the senator's wife sticking with Cross after the attempt to undermine him, Megan wakes up. Between the actual shot of her and the camera feed the sheets are touching the ground in a different way, and quite evidently the shadows cast in the scene are completely different. (00:24:00)
Continuity mistake: Cross is discussing who is in charge with Kyle, who just handed the evidence to an agent. In the same shot you can see the fed that gets in the background between them. At the cut, he's turned around facing towards the right (of the screen) while he was turned towards the left in the previous shot. And when they walk away, he has now his back turned to them entirely. (00:19:30)
Continuity mistake: Alex Cross encounters his old friend from the FBI, Kyle Craig. He briefly shows him the pieces of evidence; check out of the strap on the recorder; it is dangling in its length at first, and it is up entangled in Cross' fingers in the reverse. And Craig is holding the bagged boot in a different way (the hand is turned the opposite direction) in the two shots. (00:19:10)
Continuity mistake: After Jezzie and the principal have popped by the classroom finding it empty, Soneji is pushing the cart outside. Behind him, a couple of kids walking from left to right are walking in the path two guys walking in opposite direction, and they are ahead. But in the close-up on Michael Wincott, the two have crossed the other pair (those walking in the same direction as Soneji) walking well ahead of the others. (00:10:50)
Factual error: During the movie, Senator Rose's daughter is protected by the US Secret Service. A plot point also sanctions that senator Rose is basically a nobody, he does not hold important roles, nor he was threatened in any way before the fact. His daughter would not be under Secret Service protection then, since it is reserved only to the highest elected officials of the nation, not every single relative of every single House member.
Revealing mistake: During the botched save of agent Fisher, the helicopter with the spotlight is well behind Cross and the others, and yet the light is projected on parts of the bridge who are facing away from that light and in fact blocked by the bridge structure, as if a strong light source was coming from the front of the rescuers. (00:04:40)
Revealing mistake: In the van at the beginning of the movie, Cross is checking out newspaper clippings about the serial killer. When they are shown in close-up for a couple seconds, the two leftmost clippings, that Cross took his time to pick and hang in the van, are obviously the same article with different titles (both in a single column strip, they even have the same layout and division in paragraphs, it's easy to spot even if you don't repeatedly watch or freeze-frame to actually read, and you just need to glance to see that they even have the same author listed). (00:02:50)
Character mistake: Amongst the material collected about Cross in Jezzie's computer, there's a big magazine article related to the case of the previous movie "Kiss the Girls." The article writes in a huge font the title "The CASSANOVA killer." Not a very good magazine, misspelling Casanova like that. Incidentally, her notes also get the word "Temperament" wrong, missing the 'a', and she has a folder called "Dimitiri", getting the name of the Russian kid wrong. (01:28:30)
