Adaptation Dye-Job: Cathy Ryan, described as a classic blond, blue-eyed beauty, is now reddish-brunette.
Adaptational Villainy: Bob Ritter is a lot more unpleasant in the film version than the book - for instance, Film!Ritter is callous, smug, and eventually gets his come-uppance, whilst Book!Ritter gets off scot-free, is competent, and appreciates the seriousness of the operation he is running. Film!Ritter is also complicit in Admiral Cutter's abandoning of the Light Infantry units still in Colombia, whilst Book!Ritter is highly suspicious of Cutter's assurances that they will be rescued and helps Ryan find a way to get them out.
Armchair Military: When the operation starts to unravel and people not cleared start to figure it out, one person states rather bluntly that if the CIA had actually bothered to include the organizations they were suborning, the operation would have run smoother, would not have been discovered, and would've been a hell of a lot more deniable, basically a screed against the Armchair Military that set up the operation in the first place.
Call Back: Jack's first scene has him taking some interest in his son playing with a toy submarine.
Jack: Do you have any time in this type [of helicopter] ?
Pilot: Nine o'clock.
Continuity Nod: In PatriotGames, Sally is asked what she wants for breakfast. She says "Pancakes". Jack replies that there is no time for pancakes, it is either toast or toast. Here, in ClearAndPresentDanger, the little John Ryan, not yet born in previous movie, is asked by Sally what he wants for breakfast, and she proposes toast. He replies "Waffles". She tells him that there is no time for waffles. So he says "Pancakes". She replies "Toast".
Death by Adaptation: In the film, Moira Wolfe is murdered by Felix Cortez once she is no longer useful to him. In the book she survives, although the fact that Felix Cortez successfully got sensitive information from her results in her security clearance being revoked.
Also applies to Felix Cortez. In the film he is shot and killed by Chavez. In the book he is captured and handed over to Cuban authorities.
In the film, Ryan's FBI buddy Dan Murray is killed during the ambush on the FBI Director's convoy. In the books he isn't even present during that attack, and remains an important character in later Tom Clancy novels (eventually rising to the position of FBI director).
Even Evil Has Standards: Cortez has the mindset of a professional intelligence officer, so while he mostly has a lot of Pragmatic Villainy moments, he does show genuine disgust with the methods used by the Cartel to intimidate their rivals.
Everything Is Online: Mocked. After Cortez and Ryan both start to suspect that a car bombing was actually caused by a missile, they research the issue. Ryan, the Deputy Director of the largest intelligence organization in the world, has to pull an all-nighter alone looking through Jane's Armaments. Cortez just searches a slick, high-tech database.
Fake Kill Scare: The Coasties get a pirate to talk by blindfolding him and pretending to shoot the other one. His pal falls for it and blabs.
Infant Immortality: Averted. When the airstrike is called in on the cartel, children are seen playing in the strike zone seconds before the bomb hits. Later on the President of the United States reacts with horror when he sees news footage of child's body being removed from the area.
Mood Whiplash: When one drug lord shows up in an outlandish big-wheel truck, everyone's giggling at it including the sniper team painting it for a laser-guided missile. But then Chavez notices there are kids playing within the blast radius...
My Card: Jack Ryan has some business cards done up showing that he's the acting CIA Deputy Director of Intelligence, which comes in handy on a couple of occasions, like turning up to see Columbia's most powerful drug lord without an appointment or buying a $2 million helicopter.
The Password Is Always Swordfish: Peter, the tech person who hacks into Hardin's floppy disk (using a combination of parts of birthdays from Hardin's family to unlock the disk) and later helps Ryan remote-hack into Ritter's private terminal, correctly guesses Ryan's ATM code is his birthday in reverse.
Revenge Before Reason: The president's desire to get back at the cartels for killing his friend results in him authorizing an illegal military operation that results in the deaths of innocent civilians and American soldiers. It gets worse when Cortez stages that ambush killing the FBI Director.
Mirrored by Escobedo, who starts the whole sorry mess by killing the U.S. businessman embezzling him... plus the man's whole family, unconcerned that the businessman's friend - the U.S. PRESIDENT - might react to it in the wrong way.
Played with when Ryan reveals to Escobedo how Cortez was betraying the Cartel and his own boss, knowing full well Escobedo's rage would turn on Cortez and help Ryan recover the imprisoned covert troops.
Signature Item Clue: Felix Cortez becomes suspicious that the series of attacks on the Medellin Cartel aren't just guerrillas after finding a stray shell casing from one of the US Special Forces' team's M16s at one of the attack sites.
Smug Snake: A few, most notably Felix Cortez and Bob Ritter.
Soundtrack Dissonance: During Adm. Greer's funeral, America the Beautiful is overlaid over John Clark's team getting ambushed in Colombia.
Twenty One Gun Salute: During cuts between Admiral Greer's funeral and the ambush of the special forces. It comes to a head as the three volleys are fired at the funeral, cut against the distress calls and machine gun fire of the battle.
You Have Outlived Your Usefulness: The drug cartel intelligence officer Felix Cortez snaps Moira Wolfe's neck after getting from her the information his employer desired. Ironically, it leads to him getting discovered because the FBI agents investigating the murder found a recording of his voice on Moira's answering machine.