(at around 1h 14 mins) While fighting the goblins in their house, Helen (Jared, Mallory, and Simon's mother) does not have the sight. Half way through the fighting, the seeing stone disappears from her face, yet she can still see all of the creatures and continue fighting.
(at around 1h 13 mins) In order to kill a goblin from above, Jared pops a bag full of tomato sauce on it. He holds the bag over his head but there is no sauce on him in the next shot.
(at around 1h 13 mins) During the fight scene in the house, Jared throws several tomato bombs at the invaders. He is shown having only 1 in his hand throughout the scene. But when he throws the bomb a new one appears in his hand.
(at around 42 mins) On the way out to see Aunt Lucinda, Simon calls to Mullory and gives her an ocular device he has found that holds the seeing stone. Just before leaving the house, Mullory is seen putting the ocular device over her right eye. When Mullory and Jared first enter the tunnel, the ocular device is on the right eye as seen earlier. However, a few moments later while running through the tunnel the ocular device is on the left eye. As the two approach an intersection the ocular device is back on the right eye.
The midnight fight starts at high moon, yet during the fight several shots are in broad daylight.
If Lucinda is an aunt of the family, her father is not their great uncle. He would have to be a grandfather. A great uncle would be the brother of their grandmother/grandfather. Their great uncle's child would be a cousin of some level. Their characters are presented as great uncle Spiderwick and Aunt Lucinda.
(at around 45 mins) When Helen Grace is at her job just before she notices her children outside, she is being told by her coworker what to push on the keyboard. She clearly is pushing random keys and not the ones spoken.
When it first appears that the goblins are roasting a cat, the fire is moving in reverse motion.
(at around 5 mins) When Mallory and Jared are fighting at the beginning, Jared can be clearly seen to mouth Mallory's words.
Aunt Lucie has an American accent as a young girl in the flashback but a British accent as an old woman.