Plot hole: When Astrid gets on Toothless for the first time, Toothless takes off uncontrollably and tries to scare her. Hiccup seems to have no control over him at this time. How is that so if with the new tail fin, Toothless cannot fly without Hiccup's precise control of the tail fin? That whole sequence would have fallen apart. This mistake was even admitted to on the DVD Commentary.
Continuity mistake: When Hiccup first finds Toothless, there is a dramatic shot where the camera pans over Toothless, and his wing briefly obscures his eye, which is open after the wing passes. But look at the tip of the wing. During the shot there is a stretch of rope wrapped around it. In the next shot, the rope is much higher up the wing and not wrapped around it anymore.
Continuity mistake: In the scene where Hiccup trials his first tail fin, he gives Toothless a basket of fish. This falls off his face before he takes flight. However, the basket is never seen again; you don't see it under either wing from behind, and when he takes flight the little bit of ground he was standing on is gone.
Continuity mistake: After Hiccup cuts the ropes that bind Toothless and the dragon flies away, Hiccup gets to his feet in front of the boulder, but the ropes are gone. However, when Hiccup returns the next day, he finds the ropes very close to the boulder, where they should've been all along.
Continuity mistake: After Toothless and Hiccup defeat the giant dragon, Stoick finds Toothless on the ground and believes his son to have perished in the battle. As he is kneeling down and beginning to morn, the rest of the Vikings begin to emerge from the smoke behind him. They are a good distance away from Stoick. But in the very next shot, they suddenly jump much closer to him.
Continuity mistake: In the scene where Hiccup is in the woods looking for the downed Night Fury, right after he says "Not me, I manage to lose an entire dragon!" he hits a tree branch right in front of him and it comes back and smacks him in the face. In the next shot the branch is nowhere to be seen.
Revealing mistake: In the beginning scene when the dragons are attacking Berk, it shows several sky torch things being raised into the air. As one closest to the camera is rising, a Viking throws a burning stick at it to ignite it. If you watch it closely, you can see the torch starts burning first to the far left, well out of reach of the thrown fire. Even allowing for fumes igniting, the fumes nearest the flame should light first.
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Continuity mistake: Near the beginning, as Hiccup is chased by the monstrous nightmare, the pole he hides behind gets blasted. If you look at it, the base is made of steel plates, but after Stoick beats the dragon and the camera switches back, the metal is gone and it's just wood. There is no way it melted off and burned the wood that far and that fast.
Continuity mistake: Early in the movie, Hiccup is in Gobber's workshop. Gobber is telling Hiccup that he isn't strong enough to even 'throw one of these" referring to a weapon. Hiccup states that "this will throw it for me" motioning to his weapon throwing machine. Upon placing his hand on it, it pops open and fires, hitting a viking standing outside. In the next shot, the machine has miraculously re-cocked and reloaded itself.