Continuity mistake: Cross is cheering Jezzie up for missing her chance to stop Mercusio. He says "If you hadn't convinced me to stay there", and is gesturing with the left hand on the table...which turns into the right hand at the cut. (01:02:05)
Plot hole: There is a massive problem in the timeline of the movie, starting when the 'running game' is set. It is dawn when the kidnapper contacts the family and the police. He says, that he will call back in 9 hours, and even says "4 PM sharp." The events unfold, and Cross is on the metro train during rush hour, firing his gun. But at the press conference that follows, agent Ollie McArthur declines to comment on the "incident on the MTA train this morning." (01:03:05 - 01:10:00)
Continuity mistake: After receiving instructions from Mercusio (when Cross is told to go to the Watergate), agent Ollie McArthur says "okay people, let's move." He says that across two shots; in the first, Monica Potter is distinctly shifting her eyes from looking in front of her to looking to her right, but in the second she is looking straight again, making the lack of continuity quite obvious over such a small detail. (01:03:50)
Continuity mistake: Cross begins his running game with the kidnapper. He says "I'm on my way to Sixth and Pennsylvania.", to which Jezzie goes "I'm left and behind ya, Alex." She is from behind using her right hand on the steering wheel, but she has the left on it in the following shot. (01:05:40)
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 is at Union Station, and hears a public phone ring. When he dashes across the entrance, the passersby change between shots. (01:07:35)
Continuity mistake: Cross missed the phone call from the payphone at the station. In close-up, Morgan Freeman's hand is on top of the phone, fingertips on the horizontal side. New angle, and now he is leaning with the same arm, but the hand is relaxed, draped over the round corner. (01:07:50)
Continuity mistake: In the moments preceding Mercusio's instructions to board the train, Jezzie looks towards Cross. She is almost on her own on the platform, but in a close-up on Monica Potter, more and different people are suddenly present by her. (01:09:05)
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: After Morgan Freeman shoots out the train window to toss the diamonds out, the hole in the glass gets larger, enough for him to stick his head out easily. (01:10:00)
Continuity mistake: On the train, Jezzie says "Get down, everybody down", the two women with dark coats behind her get down twice in different ways - one is even holding a newspaper in the second shot that she did not have before. (01:10:20)
Continuity mistake: Cross is about to shoot at the window of the train to break it; he is holding on to the vertical bar of the cart with the thermos hand, but the bar is gone in the closer view. (01:10:20)
Continuity mistake: At the press conference, McArthur is going full "no comment" about pretty much anything. A grim Alex Cross is standing there. Next to him are the senator's wife and the senator. At the cut the senator disappears, leaving just the wife and the FBI agent. (01:11:10)
Continuity mistake: Cross is talking with Jezzie in her apartment, holding several sheets. The sheets are at the same height in a certain camera angle (when he says "You do what you are", and then "you were born with a gift"), despite the fact that meanwhile he moved those sheets around. (01:12:10)
Other mistake: Mercusio tazes Jezzie and enters her apartment. Look at the wall clock; the time shown is 4:05, when Cross was barely at the Watergate Hotel at that time. (01:13:00)
Continuity mistake: After Mercusio gets shot, Cross has to face the senator, who tells him "and you're telling me you haven't a clue?" The agent walking past is nowhere to be seen in the reverse shot that follows. (01:19:00)
Continuity mistake: After Mercusio's home invasion, Jezzie's ice pack turns around in her hand between shots (you can make out of the way it is pointed in the first shot when the paramedic is still checking on her; some letters are visible at the end, and they are turned straight). (01:19:40)
Plot hole: Devine is in the hideout. It is late evening/night. Nothing in the timeline here makes sense. For starters, the newscast says that "over a week ago" the manhunt for Soneji started. Cross gets on the case the first day, on day 2 they find Mercusio's home, day 3 the failed embassy run and Megan is taken away from Soneji (but nobody knows), day 4 is the jewelry heist, leaving Soneji to be killed the same day or after (the movie messes up on that account but seems to want it to happen the same day, I'd give it another day, making it 5). Moreover, it says that Soneji was killed late in the afternoon the day before; it means that Jezzie waited more than a whole day to go to him, and Devine's comment about the kid being so doped up she didn't realise she is not on the boat makes no sense when it implies she'd have to sleep for 2 days straight instead of one. (01:23:00)
Continuity mistake: Devine's cigarette burns half an inch the moment he turns the TV off (and we switch to the close-up). (01:23:05)
Continuity mistake: Jezzie points the gun at Devine's throat. When she begins laughing, she lowers the gun, which is still all the way up pressing to his jaw in the reverse shot. (01:24:00)