Common Knowledge: It is common for a post-9/11 to see Bond teaming up with the Mujahideen as a "Funny Aneurysm" Moment in part because of the belief that the Mujahideen became the Taliban and, thus, the enemies of the West in the War On Terror. This is incorrect though, because the Taliban were in fact a radical student movement (then name even comes from the Arabic "talib" which means "student") that took over Afghanistan after the Soviets were kicked out and also after the Mujahideen began fighting amongst themselves for control of the country. In other words, the Taliban and the Mujahideen are in fact enemies, and Kamran Shah in particular- being an Oxford-educated freedom fighter who casually teams up with a British spy and a Czech woman-, would probably be marked for death as soon as they took power; if anything, the real"Funny Aneurysm" Moment is that the character of Kamran Shah was most likely murdered off-screen at some point after the movie.
Ensemble Darkhorse: Necros. He's the best of the Red Grant clones, gets two sweet-ass fight scenes, has his own theme song and gadgets, and is probably the most competent and ruthless of the villains. As a result, he's very well-regarded by Bond fans.
Green Four, the BadassMI6 agent that fights Necros at the safehouse, is very popular with the fanbase.
Evil Is Sexy: Necros. The swimming pool scene. Ohsoverymuch. In fact, he's one of the very few male examples in the Bond movies.
At the beginning, Koskov is questioning Bond about the sniper Bond disarmed (Kara). Only later in the film, do we realize that he was trying to see if Kara had been eliminated to avoid revealing the truth about the "extraction".
Bond is also notably curt in cutting off Koskov's line of questioning, giving an answer that essentially lets Koskov draw his own conclusions ("I'd rather not talk about it."). Having clocked that the sniper wasn't a professional, he's got some early suspicions that all might not be as it seems with Koskov's defection.
"Funny Aneurysm" Moment: In the denouement, the Mujaheddin (in the same full desert dress and carrying *bandoliers*) burst into the room where Bond and the others are celebrating saying, "Sorry we're late. We had a little trouble at the airport."
Thanks to the War On Terror, it's hard to look at Kamran Shah without imagining him as an expy of Osama Bin Laden. Especially since his actor, Art Malik, played a similarly crazed terrorist in True Lies. Of course when the film was made, Osama Bin Laden was basically a nobody. Also, Kamran Shah is portrayed as being westernized enough to have attended Oxford University. That alone makes him very unlike Bin Laden and also unlikely to support the extremist Taliban when they come to power in the 1990s. In fact, Shah probably has a very bleak future if he doesn't get out of Afghanistan before the Taliban regime takes over.
Harsher in Hindsight: In a post-9/11 world, it may be hard for modern audiences not to view Bond's allies at the end of the film as basically being a more romanticized version of the Taliban.
It's worth remembering that the Taliban began as an anti-Mujaheddin in this movie, and the two groups were at odds in The '90s, which resulted in the remaining Mujaheddin groups throwing their lot in with the US to get rid of the Taliban. So it is unfortunate, but not as bad as you might think.
In a case of accidental foreshadowing, while showing Bond profiles of KGB assassins, Q describes one whose method is strangulation with her thighs. Ms. Moneypenny even quips to Bond that "she's just your type". (There might have been some connection, had said assassin not been a Brawn Hilda.)
Seinfeld Is Unfunny: With the Daniel Craig Bond films, it's harder to appreciate Timothy Dalton's portrayal of Bond in this film and Licence to Kill, where the producers were specifically trying to create a darker Bond to compensate for the often-hammy Roger Moore films. The difference between Craig and Dalton is that Craig's Bond completely breaks the formula, whereas Dalton's tries to recreate Ian Fleming's Bond within the established Bond movie formula.
Ironically, Dalton's more grim and cynical Bond ("If he fires me, I'll thank him for it!") was one of the things that most divided fans of the franchise at the time. In this sense, Dalton's Bond to some degree has been reevaluated as being somewhat ahead of its time.
Values Dissonance: Bond's alliance with the Afghanistan Freedom Fighters. Though, to be fair, the West is STILL allied with some of them.
Bond does get upset that said allies are pushing drugs, even if they are selling them to Soviets.
The Woobie: Kara. She has her arm injured as she pretends to be a sniper to aid her Big Bad Friend Koskov's plan to fake his defection, is arrested by the KGB, has her apartment and all her possessions (save for her cello) destroyed, and is duped into believing Bond was faking all the incredibly nice things he'd done for her to betray her to the KGB and aiding Koskov in capturing Bond by drugging him. Then she finds out that Bond was the one who gave her the arm injury, that he actually meant the incredibly nice things he did, and that Koskov lied to her. THEN, Koskov betrays her, outright tells her she's heading to a Fate Worse Than Death (by exile to Siberia). Honestly, you want to hug her by the time you get to the last third of the movie.
Oh, and her Stradivarius cello was shot.
They Wasted a Perfectly Good Character: General Pushkin was supposed to be a recurring character early on upon his replacement of General Gogol, in the wake of actor Walter Gotell's failing health. Sadly this did not come to pass, despite the standout performance of John Rhys-Davies in this film.