Aslan caused a train crash that killed at least nine people, just so that his champions from our world could appear in Narnia and bring about the Narnian apocalypse. Other questionable acts include refusing aid to an untrained child in a swordfight with a battle-hardened member of the Queen's secret police and mocking one of his followers for asking for healing. He may have an Omniscient Morality License (his author would certainly like one to think so), but as with all such characters, it can be hard for the reader to square.
Angst? What Angst?: Especially in the first book, none of them seem to miss their parents while they're in Narnia, nor do they spare much thought about how much worry they're causing everyone who knows them on Earth. Fortunately, Narnia Time keeps this from actually being an issue — but they don't know that until they're home again, which for them isn't until years later. This is partially justified, though; if they spent all their time angsting over their family and the world they left behind, they wouldn't get much done.
Common Knowledge: Despite the fact that it would be impossible for anyone who has read the books to miss the fact that Narnia is one country out of many in the other world, many people think that Narnia is the other world itself.
Ensemble Darkhorse: Out of the four siblings and main characters, it seems Edmund has fared quite a lot, compared to the others. This is probably due to the character's Anti-Hero status that he still kept even after his Heel–Face Turn.
Eustace Scrubb and Puddleglum are this too.
Reepicheep as well. Enhanced by the Prince Caspian movie.
Epileptic Trees: Scholar Michael Ward argues that there is a thematic link between the seven Narnia books and the seven major planets (see Lewis' other best-known work, The Space Trilogy).
Fair for Its Day: Lewis has taken a lot of flak for his Values Dissonance-laden statement in LWW that "battles are ugly when women fight." But other books do show that Susan and Lucy and Jill Pole are capable fighters and can hold their own in a battle. In other words, the statement is not that women shouldn't fight but that Men Are the Expendable Gender. Consider that the U.S. Military didn't allow women in combat zones until the 1990s, and not in direct combat at all until 2013.
Family-Unfriendly Aesop: The books contain the lesson that the real world is a harsh and violent place that sometimes takes a fair amount of violence to survive in. C. S. Lewis was even quoted once as saying that pretending otherwise would do a great disservice to children. Once again, an example of a very true and important Aesop, but one that many parents would rather their children didn't know.
Fanon: A large amount of fans believe that the Lady of the Green Kirtle from The Silver Chair is the same person as Jadis the White Witch. Much of this comes from a character sketch for Jadis in later editions of the books (which were not written by Lewis himself) that describes the character as "completely evil, even in The Silver Chair). For what it's worth, not much is known about the Green Lady's backstory and the only text in the book says that she was one of the "Northern Witches". Another part of the confusion comes from Barbara Kellerman playing both characters in the BBC adaptations of the books. This is ignoring the fact that several other actors doubled up and played multiple characters in different adaptations - and that Kellerman also played the hag in Prince Caspian.
Incest Yay Shipping: Well, since the four main protagonists are siblings...it was to be expected.
Mis-blamed: Some assume Susan was left out of Heaven due to pursuing "nylons, lipstick, and invitations", i.e. maturing, rather than the fact that she isn't dead yet. On the other hand, it should be noted that Jill's and Polly's (and by implication, Lewis's own) opinion was that Susan's notions of "maturity" were, in fact, immature and shallow, as Susan thought "growing up" meant going to parties and gossiping. Aslan makes it clear in Prince Caspian that growing up and actually maturing (even leaving Narnia behind for living on Earth) is a good thing. Word Of God in a letter from Lewis to a worried reader was that Susan was still alive in England and 'might very well get back to Narnia in her own time and her own way'. Susan was meant to show how one could turn one's back on Grace. But once a King or Queen in Narnia, always a King or Queen. Given Lewis's personal history, it's probably safe to say that, to his mind, those who turn away from Aslan get the chance to turn back.
Purity Sue: Lucy is considered as this by some readers, as she is (almost) always shown to be on the right and then becomes Aslan's very blatant "favorite", and the narrative keeps treating her as more special and beloved than the other Pevensies. Some Susan fans feel specially strongly about this, as they believe Susan got increasingly and unfairly shafted to make Lucy look even more perfect and unfallible. There is a case where this is averted, though, in Dawn Treader where Lucy is given a chance to turn herself into the World's Most Beautiful Woman, upstage Susan, and cause numerous wars over her beauty, a chance that she almost takes until finding she can't access the spell anymore, and realizes how selfish she was.
Real Women Never Wear Dresses: Again, Lewis's critics accuse him of pulling this in his treatment of Susan compared to the other, largely more tomboyish female characters.
Yes, it's all very wonderful for Peter, Edmund, Lucy, etc. that they get to go to heaven with Aslan and live forever in paradise. But Susan (ignoring any discussions on why) has just had her entire family, including her parents, killed in a horrific accident. May also double as Fridge Horror.
A meta-example is that Lewis wrote The Magician's Nephew in order to do, in fiction, something he was tragically unable to do in real life: save his mother.
Caspian and Rilian's reunion, as the former lies on his deathbed.
Father Christmas' assertion in The Lionthe Witch And The Wardrobe about how battles are ugly when women fight might come across as somewhat prejudiced to more feminist-minded modern readers - not that Lucy seems to care all that much in subsequent books. (And admittedly, with a somewhat more generous reading, combined with knowing Lewis' own history, it can be interpreted as a statement that "total war" is particularly ugly - since it perforce includes everyone, women included. Ol' Saint Nick and Lewis just chose their words poorly.)
Lewis' attack on secular education in the form of Experiment House may also come across this way to some readers. Though given the nature of the real-life experimantal schools on which it was based, whose ideas proved unsucessful, it's not so much the existence of the school itself as Lewis' particular criticisms of the same (such as mixed-sex education). Particularly, the treatment of bullying in-story is an inverted form of this, as any attempt to overlook bullies as "interesting psychological cases" allowed to butter up the headteacher would amost certainly have OFSTED descending on the school like a ton of bricks nowadays. It just goes to prove how radical the pre-1960s 20th century really was in ways we prefer to forget.
In general the series' overt portrayal of Christian themes has prompted something of a backlash in these more skeptical times, as an attempt to "push religion" in the form of popular children's literature. Conversely, whilst Lewis is usually well-regarded in modern evangelical circles, some more fundamentalist typesequally object to aspects of Lewis' theology and pagan elements included in the Narnia stories. The poor man can't catch a break either way.
On this note... the Calormenes. Oooooh, the Calormenes. Who are, you know, barely-concealed expies of real-life Turks and Arabs, and who worship "Tash", who invokes damn near every hateful, negative criticism of Islam and Allah from fundamentalist Christians. Of course, in Lewis' time, these stereotypes were relatively common ideas when American & European people bothered to think about that part of the world and Islam at all (remember, even toward the end of Lewis' life the Arabic oil fields were only starting to become a big deal) and weren't seen as particularly controversial. In the 21st century?... well, either you're one of the certain set of people who love the idea of hating Muslims and thus really dig Lewis' implications (when he probably didn't actually intend that much vitriol, as he does seem to have drawn some inspiration from Arabian Nights and isn't completely unsymapthetic to Arab people), or you're made really uncomfortable by the essentially-unmasked anti-Arabism and Islamophobia.
The Professor's assertion that anyone could tell Lucy isn't insane by looking at her now comes across as really ignorant about mental illness - but, especially during the time the work itself is set, would have been a nearly-universal opinion.
Foe Yay: Between Edmund and the White Witch, especially in the The Voyage of the Dawn Treader film. He's haunted by visions of her on and off throughout the journey, taunting him about how he's trying to prove his worth. It gets especially explicit when she repeatedly offers to make him "her king", and that she can make him a man. Some of the things she says are borderline Mind Rape, stating that she'll always be alive in his mind despite the fact she's died arguably twice now (the second time by Edmund's own hand). Considered Squick by some for obvious reasons.
Mr. Tumnus. He lures a little girl into a small dark cave, lulls her to sleep with a flute, and when she wakes up, he's crying and saying he's been doing something bad.
The White Witch. Wrapping Edmund in her fur with her, being all close, asking Edmund to come to her castle, and to bring his siblings too. Jeez lady, and to only up the creepiness with Edmund, in the third movie, constantly whispering almost seductively, "Edmund, I can make you my King... and much more."
Without knowing he was going later be resurrected, Aslan's death scene in The Lion, the Witch, and the Wardrobe. The great, proud cat being bound and getting his mane hacked off, knowing he is sacrificing himself for love shows simply how realistic and emotionally well done the death scene was. The parallel too.
The BBC version, however, is a completely different story. The buildup is sad, but the death sequence is ruined by The White Witch's acting (and the...shall we say, less than stellar animation).
Athough it does provide Hilarious in Hindsight value when you compare the White Witch's potrayal throughout the entire BBC production with Xenia Onatopp's similar portrayal. Heck, you could even argue Xenia was inspired by the BBC White Witch!
And, precisely because you know what's coming, Peter and Susan's walk with Aslan near the end of Prince Caspian, and Peter's subsequent acknowledgement to the others that he would not be allowed to return to Narnia.
The final scene in Prince Caspian when the Pevensies leave. Throughout the movie you see the devastation the four of them have suffered at being ripped from Narnia and back into the normal world. And now they've finally come home again they have to leave. It's utterly heartbreaking and you realize that no matter what anyone says, or how old they grow, they're never going to recover from losing Narnia.
And when Lucy glances back, Narnia's just...gone.
And the music doesn't help either. The lyrics are simultaneously perfect and horribly bitter.
"I'll come back...When you call me...No need to say goodbye...No need to say goodbye...
On a similar vein the end of the The Voyage of the Dawn Treader. Lucy and Edmund just look at each other and at the painting, suddenly realizing that's it. No more adventures, no more Aslan, no more magic: they're trapped in the normal world forever.
The end result of storming the castle in the Prince Caspian film is absolutely devastating - particularly the moment in which Peter looks back through the portcullis at the trapped Narnians, and at least one voice is clearly heard calling for him to save himself.
You see the Narnians at the gate, all screaming and trying hopelessly to get out, and you know that each and every one of them is dead. And the look of anguish on Peter's face as he realizes the same thing, and there's nothing he can do about it...
Props also to the brave Minotaur who held the gate open for as long as he could, only to be shot and crushed under its weight—a Heroic Sacrifice which saved many of the heroes, made even more poignant when one remembers that Minotaurs were "evil" in the first movie.
Lucy's goodbye to Aslan in The Voyage of the Dawn Treader. Made especially more poignant, when you remember that Lucy was the first of those siblings to find Narnia.
Eustace's goodbye to Reepicheep. Considering the development their relationship has had throughout the movie, that scene was heartwrenching.
The simple line from Eustace's narration - "When the war ended and my cousins went home, I missed them"
Unpopular Popular Character: Edmund Pevensie is the biggest example. He's the black sheep of the family in the first book, The Unfavorite and the villainous sibling from the main four, as he betrays his siblings to the big evil and torments and bullies Lucy. He easily becomes most fans' favorite character by the end of the second book and movie.
What an Idiot: Granted, Maugrim didn't think that Peter had it in him to kill, but that doesn't mean that jumping directly onto Peter's sword was a smart move.