Factual error: A bunch of troops are in heavy camouflage in helicopters, going to an assignment. The officer in charge tells them to take their dog tags off and empty their pockets of anything that could identify them. This is silly: first, in troop helicopters, the troops wouldn't be able to hear the officer's voice - it's too noisy - and second, this would be ingrained in them, to remove dog tags etc, and would have been done back at the base, before they left.
Continuity mistake: When Jack Ryan is in his office and hacks into Ritter's computer, he is trying to print out some files before Ritter deletes them. His printer fails to print, and after pulling out the paper drawer of his printer he discovers it is out of paper. Immediately, without closing the drawer, he quickly opens the door to the cabinet beneath the printer, grabs some paper, and the very next shot shows the printer paper drawer has mysteriously closed, so he has to pull it out again to add the paper.
Revealing mistake: When Jack Ryan goes to Ernesto Escabeda's residence and asks to see Ernesto, as he is led up to the house we see his two companions on a roof top ledge watching through binoculars and one of them says "He's in", if you look at that shot closely the suppressor on the mp5 laying next to the sniper is fitted at a decidedly wonky looking angle.
Revealing mistake: There is a scene where the Army team is moving through the Colombian jungle. At one point one of the team members has the muzzle of his weapon pointing straight at the camera. You can clearly see the Blank Firing Adapter (BFA), a shiny brass looking thing, in the compensator of his M-16.
Revealing mistake: There is a scene where a jet flies over a city which the movie states that is Bogota, Colombia. But those who have been around South America will notice that this scene shows Quito in Ecuador, not Bogota. This doesn't only happen in that scene, but also at the airport scene where the jet lands. You can notice a couple of Ecuatoriana 707s as well as some other Ecuadorean airliners in the background. Also, if this were El Dorado airport in Bogota, you wouldn't see Pichincha mountain, first of all, and secondly Pichincha wouldn't appear so close to the airport as it does if this were to be Bogota.
Other mistake: The first plane to explode has a very neat symmetrical blast originating from underneath the plane - which is in fact wrong given that only one charge was placed on the side of the plane. The plane would be badly damaged and probably jack knife through the side of the hangar instead.
Continuity mistake: During the scene in which the convoy of CIA Suburbans is ambushed from the rooftops, Harrison Ford and the remaining men get back in a Suburban that has already been hit and the driver's door is missing. Ford hurriedly jumps into it and begins backing out of the ambush. Even though he didn't buckle it, a seat belt is visible around him. When he jumps out of the Suburban, he doesn't unbuckle the seat belt.
Continuity mistake: A Hawker 125 executive jet lands with the guys who are eventually involved in the street ambush. The hangar scene where Ryan greets them getting off the plane has them deplaning from a larger Gulfstream executive jet.
Plot hole: The plot of this film relies on the notion that Cutter and Ritter (with the backing of the President) are able to conduct this illegal war against the cartels with this small team of soldiers blowing up planes and drug bunkers while making it appear to be coming from rival cartels. OK, fine. The problem though is when you bring an aircraft carrier into the story a lot more people are going to have to know what's going on that are not in the loop. You would have admirals, navy officials, possibly even the Joint Chiefs wanting to know why planes are taking off from one of their aircraft carriers just outside of Colombian waters. It didn't take Ryan any effort to find the operations report on the "car bomb" and put two and two together, so I find it very hard to believe none of the higher ups in the Navy were questioning Cutter or the President as to what was going on.
Visible crew/equipment: When the Coast Guard Captain is looking through her binoculars at the yacht the camera switches to the binoculars' point of view to show the yacht in the distance. The front of another boat is visible just below the back of yacht, this couldn't be the front of the coast guard vessel so it would have to be whatever the film crew was using to get the binoculars' point of view of the yacht probably just a few feet away.
Factual error: It wouldn't have mattered that Ritter had his "autographed get out of jail free card" given to him by Cutter or authorized by the President, it was still an illegal operation that Congress didn't know about. Anyone involved in it would be going to prison regardless of position.
Continuity mistake: When Ryan confronts Ritter about Reciprocity in the office, the view switches from behind Ritter to in front of him. Look at his suit coat collar. When he pulls the President's letter from his safe, the collar is fine. As the view changes, the coat collar is flipped up on the left side.
Plot hole: Given the lengths that Escobedo is willing to go deal with people who have wronged him it's pretty hard to believe he would have wasted his time imprisoning the rest of Clark's team instead of killing them, especially after they caused so much damage to his cartel.
Other mistake: In Colombia, a heavily camouflaged soldier goes into a hangar and places a bomb on it and rushes out before it explodes. On his way out, he passes another soldier who is lying as close to the ground as possible. In front of this soldier is a line of fine wire, right in front of his face. The only thing I can think of for that wire being there is as a marker for the actor.