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.
Merlin, meanwhile, spends the film on a vengeance quest to destroy an entire religion because he's angry at one goddess (though he knows that the other members of the pantheon are good), becoming a knowing accomplice to a rape in order to help achieve his goals. He then complains that men don't live up to his lofty moral standards.
Big Lipped Alligator Moment: The cutaway scene of Queen Mab and Frik dancing (for a very loose definition of dancing). The latter you might forgive, but the former...
Complete Monster: While most of the villains have some redeeming traits, Vortigern goes all the way. In addition to being a tyrant and a power-hungry conquerer, he takes the daughter of one of his most loyal lords captive and threatens to kill her himself if her father doesn't behave, just because he doesn't trust anyone, and casually refers to having murdered men, women, and children just for mouthing off to him.
Mordred is even worse. He injures or murders castle servants while practicing archery, shoots arrows at everyone in the room just because one of them commented that his performance was "less than perfect," acts disturbingly excited and pleased at the thought of Elaine's heartbreak, laughs at his own mother's death, starts a war and plunges Britain into chaos, etc. In the novelizations, his evil is stepped up a notch, and his motives border on Chaotic EvilOmnicidal Maniac doing it For the Evulz.
If forgetting Queen Mab is the only thing that can ultimately defeat her, then isn't Merlin shooting himself in the foot by spending the rest of his life telling stories about her?
Though it becomes Fridge Brilliance if you consider that the decline of the Old Ways and Mab's death in particular were very bittersweet for Merlin. He may be trying to keep them alive despite himself.
In the novelizations, Merlin doesn't include Mab in any of his stories, instead attributing her deeds to Morgan le Fay or Mordred, and Frik does the same thing. This is implied to be the thing that Frik noted was "omitted" from Merlin's story at the end.
Maybe he took a page from Terry Pratchett? When you tell stories about something, people know about them more, but believe about them less. Tell magical, fantastical stories about the Fair Folk today: next stop, nursery wallpaper.
There's also the fact that the stories would be telling people about Mab...but that she used to exist, and would include the ending in which she faded away. So even as they told people of Mab they'd be reinforcing the fact she is just a memory, a thing of the past.
So, Galahad was the real Chosen One, instead of Lancelot. So, a 10-year-old boy was supposed to win the joust?
Had Merlin known that Galahad was The Chosen One he wouldn't put a kid in a jousting match. Also, it's that he would be the perfect knight when he was grown up, not as a kid. It's not suggested that he has to win a jousting match anyway, just that he has to be a man of pure heart.
If changing form is just an illusion then Merlin and Nimue will still be dead in a few years despite Merlin's apparent youthening of them both at the end.
It's only an illusion when the Fey do it. Merlin used a different kind of magic to do that. It's explained more in the novelization.
If Frik can see so far into the future as to know about early modern French aristocrats, he should also foresee the inevitable triumph of Christianity in Europe.
Time can be rewritten. Presumably that was what he was aiming for.
At one time Frik is shown writing fairy tales, so that Mab and he will be remembered. Mab is dismissive of this, but Frik seems to keep all options open. Perhaps he has seen the triumph of Christianity.
Jerkass Woobie: Morgan le Fey grows up insecure about her lisp and drooping eyelid. She witnesses Uther rape her mother via Bed Trick, then murder her father and his men, all because Merlin let him. Later, she's used as a pawn by Mab and Frik, and eventually her son completely stops caring about her in preference for a surrogate, "Auntie" Mab, who kills her in the end. On the other hand, her reaction to the childhood trauma is bitterness and eager complicity in the plot to screw over Arthur, and she probably has a lot to do with Mordred's poor character.
Moral Event Horizon: Vortigern casually referring to having killed men, women, and children simply for insolence, or deciding to sacrifice Nimue to a dragon simply because it was most convenient.
For Mordred, this moment is probably when Mab kills Morgan le Fay, and he responds by laughing about it and complimenting her on it. “That was very clever.”
Tear Jerker: The deaths of Ambrosia and later Arthur, and their final words with Merlin. Also, How Frik's relationship with Morgan le Fay ends.
The Lady of the Lake's final conversation with Merlin, and the lingering demise of both Queen Mab and Magic.