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.
Alternate Ending Interpretation: Was Ofelia rewarded for her integrity at the end, when the king and queen of the underworld say that that because she refused to spill the blood an innocent, she passed the final test, or was the "blood of an innocent" required, referring to her own blood? Which ending you decide determines how much sympathy you have for the Faun.
There's another alternative for those who view the film more on the "mundane" side of Maybe Magic, Maybe Mundane. The end is merely Ophelia's dying, blood-loss induced fantasy.
Award Snub: Subverted. The film did quite well come Oscar time, winning for Art Direction, Cinematography and Makeup. However, it ended losing Foreign Language Film in an upset to The Lives of Others. Not the worst case of this, given how the latter film is also quite great.
The film also failed to earn a Best Picture nomination, despite appearing on more Top 10 lists than any of the actual nominees that year aside from The Queen and The Departed.
Complete Monster: Captain Vidal is far more terrifying than the fantastical monsters in the same work and one of the most terrifying examples of this trope. Vidal first shows his nastiness when two poachers, a father and son, are brought to him in the dead of night, his men suspecting them of being rebels against the regime. He beats the younger man's face in with a bottle simply for defending his father against Vidal's accusations before shooting them both with a vague air of boredom and pleasure. When the men are proven not to be rebels, Vidal shows no remorse, only belittling his men to be more careful next time. At one point, Vidal captures a rebel with a horrible stutter and cheerfully shows the man his torture instruments before offering to let him go if he can clearly count to three. He fails. Vidal is married to the young heroine's mother solely so she'll bear him an heir, and shows no concern over the possible death of his wife in childbirth. When the doctor attending her gives the aforementioned stuttering torture victim a mercy kill, Vidal coldly guns him down. At the film's end, Vidal's stepdaughter Ofelia tries to rescue her baby brother, but Vidal catches her and promptly shoots her fatally. It's no accident that Vidal's place at the head of the table in the dinner scene parallels that of the Pale Man; each qualifies as a Monstrous Humanoid in his own way, one literal, one figurative.
Death of the Author: Despite del Toro's own insistence that the magic is real, some viewers hold that the film is better assuming Ofelia is simply delusional, and merely using the Faun and the fairies as a coping mechanism for her own traumas.
Genius Bonus: Pretty much every single event in this film is based on an existing folk tale, even the wraparound story. This film is literally folklore wrapped in folklore sprinkled with more folklore which will evoke a strong "don't open the door!" type of terror from those familiar with the source material. Yes, even the crazy stuff regarding chalk doors and mandrake roots have actual folklore magic roots!
Word of God has confirmed that his idea of Pan is far too wild and dangerous to serve in a role of the Faun (Which makes sense, considering the actual mythology behind the God Pan, who is often described as hypersexual or even paedophile.)
Moral Event Horizon: Vidal beating a boy's face in for supposedly being a rebel is one of the most horrific scenes in the entire movie. It is also one of the first centered on him. And he only gets worse from there.
Narm: The Pale Man seeing with his eyes in his hands (which also happens to be the image in the Nightmare Fuel entry of the film), and the King of the Underworld (a.k.a. Ofelia's dad) being an old man with a white beard could fit.
Nausea Fuel: The poor sap getting his face beaten in by Vidal, and that's just the tip of the iceberg.
The sickening sound as the Doctor begins to cut into the injured man's leg with a saw...
The first task, with the frog in the tree. All of it.
The bloody face of the poor rebel who was interrogated.
One-Scene Wonder: The Pale Man only shows up once, yet for many people, he is the most memorable thing in the movie.
Squick: Both supernatural (the Pale Man) and mundane (Captain Vidal getting his cheek cut open and subsequent sewing it back together.)
And to add to the Nightmare Fuel factor: After Vidal provisionally sews together his cheek, he takes a quick gulp of whiskey (or some other high-percentage alcohol.) He does not manage to swallow it all at once, and there is a painful sequence, where whiskey comes flushing out of his sown-up cheek. And one can only imagine the intense pain of having an open wound at the mouth flushed with concentrated alcohol, in this case a searing bitter. Strangely enough, this short moment occurs without much blood spill, which in fact makes it all the more... Squick.
Visual Effects of Awesome: It's probably close to impossible to overstate just how awesome the film's effects are, but it's worth noting that it won multiple Oscars for them (Best Art Direction, Best Cinematography, Best Makeup,) as well as tons of other awards.
What an Idiot: Much like many a child fairy tale protagonist, Ofelia suffers from Genre Blindness by eating from the forbidden feast. Even after she is told repeatedly not to eat from it, with her fairy guides trying to stop her from consuming the grapes, as well as the Pale Man sitting right there at the head of the table. Though, it may have to be taken into account that she hadn't eaten in at least a day and since it was faerie food, it could have very likely been enchanted to be irresistible.
The former explanation is seemingly confirmed in Guillermo del Toro's Cabinet of Curiosities. Del Toro comments how he regrets cutting out a line that explains that Ofelia hadn't eaten in a while, thus explaining how easily she fell to the temptation.