These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Clear and Present Danger
Harsher in Hindsight: How much Clancy got right about the drug war in Columbia is borderline prescient. To start with, Operation CAPER involves intercepting cell-phone calls in order to gather actionable intelligence against the cartels; in the 80's to the early 90's, American ELINT-gathering units of the ISA, then known as Centra Spike, were crucial in dismantling the operations of the biggest cartel in Columbia at the time, the Medellin Cartel. Next, it is decided to make the laser-guided bomb strikes against significant cartel heads look like the actions of disaffected anti-government guerillas; in real-life, vengeful vigilante groups like Los Pepes began to lash out against the cartels as the body count from narcoterrorist acts began to rise. Then, Escobedo, an expy of the real-life Pablo Escobar, is brought down by the light infantry team headed by John Clark. The real-life Pablo Escobar was killed in a raid by a unit specially trained by US Special Forces advisors, with the very real evidence that those same advisors had taken part in those raids (it is speculated that Escobar was actually killed by a Delta Force sniper covering the Columbian assault team).
A covert operation to make surgical bomb strikes on enemy High Value Targets that result in civilian casualties and political pressure on the current administration? Had Clancy written in that they were being dropped by drones, this would have been downright eerie.
Literal Genie: Cortez confesses everything after he's captured in exchange for immunity from US prosecution, since trying to figure out which laws he broke would've involved a huge political mess. So in a gleefully ironic moment, he's "repatriated" to the Cuban intelligence service that taught him all of his tricks and that he betrayed.
Magnificent Bastard: Cortez, Cortez, and again Cortez. The man very nearly gets away with manipulating several drug cartels and the US forces sent to hunt them by playing them like a fiddle. He's no coward, either: his Crowning Moment of Magnificent Bastardry involves setting up an assassination attempt on himself and then manipulating the cartel into trusting him. Holy shit.
In the film, Ritter gets his due. He insists on a signed letter beforehand knowing full well how these covert ops go bad to cover his own ass, and when Ryan confronts him with what he knows Ritter breaks out his literal "Get Out Of Jail Free" card and taunts him with it, knowing that while he is covered Ryan (who's been set up as the Fall Guy) isn't.
One-Scene Wonder: In the film there is an unnamed gray-haired security agent who is present during the ambush on the FBI director's convoy. During the ensuing gun battle he proves himself to be very brave and competant, and heroically sacrifices himself to help Ryan and the others escape. He was only in the film for a few minutes, but he was enough of a Bad Ass for people to remember him.
What the Hell, Hero?: the US uses a lot of morally questionable and highly illegal methods to combat the drug trade, and some of the methods actually work. On a smaller scale, law enforcement agencies—the Coast Guard and an Alabama police department—use similarly extralegal tricks to bring about justice, and the climax features Jack Ryan and the Pave Low crew disobeying orders to rescue the soldiers. Clancy notes that success doesn't justify the illegal nature of many of those actions.