Lady Van Tassel getting hoist by her own petard in the end makes perfect sense if you follow modern Wicca, which holds that whatever energy you send into the universe comes back on you threefold, for good or ill—in other words, happy stuff goes in, happy stuff comes back... angry stuff goes in, angry stuff come back, and so forth. Lady Van Tassel uses witchcraft to send the Hessian on a bloody killing spree for her own revenge plot, and it snaps back on her so hard that she gets dragged, alive, into the twisty Burton tree that the Hessian used as a gateway when he did her bidding.
The extreme flammability of the windmill might have seemed like typical Hollywood special-effects overkill to some, but in fact it's very realistic. Flour mills are subject to the same problems coal mines are: the flammability/explosive qualities of combustible dust suspended in the air. These can cause very serious explosions, with one flour mill explosion in 1878 having killed 18 people. Even today with all our modern technology, there's roughly a dozen dust explosions per year in the agricultural sector.
Ichabod's "chemical test" which supposedly was able to tell him that the beheading was one clean cut seems incredibly bogus, as there's no way a simple powder reaction could give him such an answer scientifically. But when one recalls his mother was a witch, it makes more sense. Magic is in his blood, and he doesn't even know he's using it.
Or the powder reacted to the blood, which would be hidden by the leaves, making it show up clearer, showing there was only enough spray for a single swing rather than a mess of hacking (it is harder to cut off a head than most media shows), you can tell alot about a crime scene by blood spatter.
Why does Katrina give Ichabod the book? So that if he finds an unusual symbol drawn under his bed or anywhere else in the house, he can look it up and know she means no harm.
And the reason he didn't read the book sooner was because he thought it was just a book about witchcraft, never suspecting it was actually a book on counter-acting witchcraft. It was only once he looked inside the book that he discovered the protection spell that showed Katrina's true, kindly nature. As obvious a pun as it may sound, it reflects his biggest flaw: he judges books by their covers.
Why does Lady Van Tassel murder the servant? In addition to needing a female body to pass as hers, Sarah would also know that Lady Van Tassel busted her and the doctor having an affair and could give Ichabod vital clues if he asked her. Sarah notably 'disappears' before Ichabod can start asking any questions.
Lady Van Tassel's curiously un-emotional reaction to the news of Hardenbrook's suicide takes on another dimension after the reveal. She probably killed him herself.
The Hessian clearly had some standards, given that he wouldn't hurt two little girls he found in the woods. Lady Van Tassel forced him to behead an unborn fetus and a little boy.
Of course, he might not have hurt the girls because he needed them to be quiet. If he would've gone after one, the other most likely would've screamed and he cannot kill both at once without making a sound.