Continuity mistake: In the scene where Hogsquel gives Jared "the sight", after he spits in his eyes Jared is holding the seeing stone, but in the next shot when he is wiping the spit from his eyes the stone is gone.
Continuity mistake: When Jared and Mallory are running through the tunnels, Mallory's eyeglass switches to the left eye in one shot.
Audio problem: When Jared is arguing with his mom in the car, his mouth isn't moving.
Continuity mistake: After Jared and Mallory visit Lucinda, back at the house when Mallory takes Jared outside to show that the goblins are gone, she is not using the seeing stone. Then she reacts when Hogsqueal approaches as if she can see him but in the next shot she acts like she can't see him.
Suggested correction: Actually she's reacting to hearing him, not seeing him, which is why she asks who Jared is talking to.
Revealing mistake: When Jared is first reading the field guide, in flashback, there is a shot of Mulgarath in crow form trying to take the book from Arthur Spiderwick. Later in the movie, when Jared is about to burn the book, the same shot of Mulgarath is used again.
Continuity mistake: In the scene where the kids are outside in front of the house, and maybe elsewhere, the double they used for Freddie Highmore is shorter than him, so when they're panning from one brother back to the other's back for dialogue scenes he's changing height between shots.