Adaptational Badass: Rhita Gawr is a very obscure character from Arthurian mythology—he was a king (and possibly a giant) who defeated other kings, cut off their beards to humiliate them and made them into a cloak. Arthur killed the guy. In this series, he's the king of evil spirits and basically wants to conquer the universe. See Hijacked by Jesus below.
Anti-Magical Faction: Clan Righteous, who used the Anti-Magic Negatus Mysterium in their quest to destroy all magical creatures and magic users, along with creating kreelixes, demonic beings who specifically hunt them.
Big Damn Heroes: When the Slayer goes after Merlin and the kids, Shim grabs him and tosses him far out to sea, admitting he wanted to crush him, but the Slayer's arm swords were cutting into his hand.
Big Eater: The Living Stones are rocks that lie dormant until someone happens across them, and then they eat that person/thing. Grand Elusa is a large spider woman who, while helpful, really advises you to leave when she gets hungry. She saves the heroes from the original encounter with living stones by eating one.
Cyclops: Balor. Made worse because his gaze can kill you.
Dark Is Not Evil: Domnu, who is described as being cold but not evil, like her other name, Dark Fate. She can be kind of a jerk, though.
Disability Superpower: Merlin is blinded in the first book, but then develops "second sight," which seems to be a kind of magical version that doesn't use his physical eyes. It also means that he can occasionally see things that normal sight cannot.
Easily Forgiven: Played with for Dinatius the Slayer. He murdered numerous innocents and blames Merlin for his deformities, which were his fault to begin with. Merlin opts to forgive him despite all of the tragedies, because he wanted to break the Cycle of Revenge, and that he pitied the slayer for having hatred consume him. Dagda restores his arms, but does not grant him wings like the other humans, reasoning that he has caused too much harm.
The first book has the Ghoulians, undead warriors of Stangmar that pull swords and daggers out and cast them aside like they're nothing, and even get up after a very angry giant stomps on them over and over again.
The Wings of Merlin has Slayer, who uses any spell Merlin uses to attack or flee back on him, and even goes through a desperate Stangmar, survives being crushed in Shim's giant hand, comes back after being thrown out into the sea, swims through the sea after Merlin escapes on a boat to an island surrounded by a magic barrier, proceeds through said barrier, and even survives a rock slide on top of him.
In Name Only: When you get down to it, most of this series (including the entire setting of Fincayra) is standard fantasy with a few brief references to Athurian legend. The Mirror of Merlin is a bit closer though, as it involves time travel, allowing Merlin to meet a young Arthur and his own future self.
Merlin and Nimue: Nimue appears as a minor character in The Seven Songs of Merlin; she flirts with Merlin and tries to steal his sword, but gets beat pretty easily. Her future self is the Big Bad of The Mirror of Merlin and plays the trope straight, being the one who trapped Future!Merlin in his crystal cave. However, Future!Merlin says his younger self can learn from this and avoid that fate.
Never My Fault: Dinatius and the bullies try to burn Merlin's mother, they fail when Merlin attacks them, and the fire consumes them. Dinatius begins to murder innocents and blames their deaths on Merlin because his near-death experience allowed him to serve Rhita Gawr.
The Stars Are Going Out: This is a big part of the The Great Tree of Avalon sequel series. In the first book, the stars of the constellation of Merlin's staff go out, so the characters seek a way to travel to the stars to relight them.
Trilogy Creep: For the first two books, the series was advertised as a trilogy. With the third book, it was decided that two more would follow and the billing for the series became an "epic" instead. In the introduction for the third book, the author states that Merlin himself told him that three books would not be enough. This isn't quite so galling, though, when you consider that in the introduction to the first book, he states that the story came to him through Merlin.