Family-Unfriendly Aesop: In book 2 of ''Beyond The Spiderwick Chronicles, Laurie explains that she lies because "lying works," and nothing in the story contradicts this claim. This, from a book aimed at 6-12 year olds.
Hilarious in Hindsight: So let me get this straight; this is about a pair of preteen twins who discover an old journal, which was written by a relative who disappeared years ago, that doubles as a guide to the secret mystical world around them? That sounds awfully familiar...
Mulgarath and his unnatural eyes is an incredibly nasty customer in just about any of his forms, though his native (ogre) form wins the prize for sheer ugly. The goblins and trolls aren't exactly going to win any beauty contests, either.
"Click klack; watch your back"
The Banshee from the field guide.
The field guide, especially the troll descriptions.
Anytime a character has to face goblins or other unfriendly without the stone or hobgoblin spit to let them see them.
The fairies drowning in honey in the last book. Jared saves a few but is traumatized by the experience.
The third book introduces Unicorns to the series, something which would be wonderful if it weren't for the fact that the unicorn in question shows Mallory and Jared a vision of why there are so few unicorns (and faeries in general) left: human hunters killing them for their pelts and horns. This is described in an incredible amount of detail for a children's book.