At first, the state of the ongoing war between humans and trolls seems to contradict Morgana's statement in Trollhunters that it was her that instigated it. However it is revealed here that it was her failing to protect Guinevere that led to Arthur's crusade against all forms of magic, so in a way she actually was responsible, just not intentionally like she claimed. Morgana at the time takes full responsibility, telling Claire that she blames herself for Gwen's death and how Arthur has changed.
In Trollhunters, Merlin explains that Morgana is as ancient him, or perhaps more so. It was initially believed he meant Morgana was older than Merlin, despite their appearances. However, Wizards implies he was actually talking about Morgana's magic being more ancient than his, which would make sense since Morgana was resurrected by ancient sorcerers whose magics are more ancient than Merlin's.
The fact that the Arcane Order's champion cursed Jim with a rock that will make him a full troll rather than outright killing him seems like a case of Complexity Addiction... until you remember that doing so would simply result in the amulet choosing a new Trollhunter, giving them another enemy to fight. The curse used seemingly makes Troll Jim more susceptible to being Brainwashed and Crazy, giving them another minion, depriving Merlin of his champion and access to the amulet in one fell swoop.
What's more, it's been established that only the Trollhunter can activate the amulet (with the exception of Merlin, who made it and thus knows all its tricks), which may have been required for the ritual to resurrect Morgana. Thus, brainwashing Jim gives them an extra layer of insurance so that they can use the amulet for their goals.
Blinky once established in Trollhunters that just before the Battle of Killahead Bridge, AAARRRGGHH!!! renounced his Gumm-Gumm ways and that if it weren't for his aid, the outcome of the battle would've been drastically different. As a general, AAARRRGGHH!!! would know the strengths and weaknesses of Gunmar and his army, hence why Vendel believed Blinky should be in charge of and tame him. As soon as Deya readily accepts her role as the Trollhunter, the trolls of Dwoza begin plotting and use AAARRRGGHH!!!'s knowledge of the Gumm-Gumms to up themselves against them and win the battle, hence why The Cavalry Arrives Late.
There is a stark contrast between how Gunmar and Arthur attempt to brainwash Jim. When Gunmar used his cursed blade on Jim, the latter manages to resist through sheer force of will, as Gunmar was trying to possess Jim's mind. Arthur, however, possesses Jim's heart by stabbing him with an onyx shard. It's no wonder Beast Jim is having so much trouble fighting back; Arthurinjured his heart and his force of will alone is not enough to heal it. It's more apparent when Claire finds Jim's human soul in the Shadow Realm, begging her to help free him.
