When Ichabod is brainstorming the connections between various events and writing them in his notebook, the individual words that are shown being written are in a different handwriting than when they appear all together on the page.
(at around 49 mins) When Ichabod cuts up the tree and is splatted with blood, it is on his face and down his neck and white shirt. During the cutting of the tree, the blood splatter on his face changes position with each shot. While digging the hole and following the headless horseman, there is no evidence of blood on his shirt.
Ichabod, Katrina, and Young Masbath bar the door of the windmill with a shovel and put two sacks on the left side of the door and one on the right. However, when Ichabod says "To the roof; I've got an idea!", there is only one sack on the left side of the door. When the horseman cuts the shovel with his sword, there are again two sacks on the left side of the door.
(at around 53 mins) When Thomas Killian is spinning the lantern with cut out shapes, the lit-up shapes on the walls are spinning in the other direction.
When Ichabod is riding in the carriage to Sleepy Hollow he pulls the window shade down after the howling of the wolf. When the camera focuses on the carriage from a distance, the shade is no longer down.
Ichabod Crane performed autopsies on cadavers and these bleed in spurts. When a person dies, all the blood inside the body quickly coagulates.
When Ichabod is in the carriage and about to leave town, he is playing with the cardinal/cage optical illusion toy. When the camera faces him the image of the cardinal and cage are right-side up, but when shown from Ichabod's view they still appear right-side up. One of these two shots should show the images upside down.
(at around 18 mins) In the flashback showing the death of the horseman he is shown being buried still wearing his combat armor yet when Ichabod digs up his grave in the present (at around 50 mins) all that remains of him is a bare-boned skeleton. Having only been buried for a decade or 2 there would not have been enough to completely decompose the armor to nothing since it was made of cured leather and metal.
The capital of New York state moved to Albany in 1797. After that date, any investigator would have come from Albany, not New York City; although as justice at that time was administered locally, it is unlikely that any "state" investigator would be sent, anywhere.
Peter Van Garrett's marriage certificate names him as being wed to "Miss Emily Winship, maiden." However, Emily Winship was known as a widow and would therefore have been referred to as either "Mrs. Emily Winship" or (more likely) "Mrs. [dead husband's name] Winship." She would most certainly not been referred to as a "maiden," as the term was synonymous with "virgin." In those days, any woman who had ever been married would have been exempt from the term "maiden."
(at around 23 mins) There is no way a chemical test could reveal how many thrusts were used to decapitate that man's head. Of course there isn't, but it was included in the film as a humorous way to illustrate how Ichabod's unconventional techniques give him unrivaled detective skills.
In the opening scene, when the little boy is lighting his candle to see the figures on the wall, he sits very close to the candle. So the light from the figures should be visible not only on the wall behind the boy, but also on the boy himself. This does not happen.
(at around 2 mins) At the very start of the film Peter van Garret in the carriage is looking forward in the direction of travel. He looks out of his left-hand window at a scarecrow. The camera tracks the scarecrow as the carriage goes past. The tracking shot is not correct. It is a tracking shot as filmed from the right-hand side of the carriage, but Peter was looking out the left-hand window.
When Baltus Van Tassel is standing on the elevated platform inside of the church, the Headless Horseman is circling outside plotting his next victim. The Horseman grabs a rope, breaks off a piece of the fence, ties the rope around the baluster, and throws it through the huge window behind Baltus without breaking a pane of glass.
When the Hessians horse is killed during the backstory, the rider is clearly a stunt double.
The New York Police Department of which Ichabod Crane is a constable was not founded until 1844, and the dark blue uniform was not issued until 1853.
When Ichabod Crane embraces Katrina van Tassel, the sleeve on his arm is pulled back slightly, revealing a wrist watch.
Flashbacks have the 7-year-old Ichabod seeing an iron maiden. If Ichabod is at least 25 in 1799, then this scene takes place in 1781 at the latest. This torture device is therefore a minor anachronism, as it was invented (primarily for display in museums) only in 1793.
At Van Tassel's party, carved pumpkins decorate the mantelpiece. The tradition of carving pumpkins was not commplace in America until the great Irish immigrations of the 1840s.
The embalming process discussed in the movie was not developed until the 1860s.
The closing credits thank "The Town of Hertsfordshire". The correct spelling is Hertfordshire (commonly abbreviated to "Herts"), and Hertfordshire is not a town, it is a county. There is a town but it is just called Hertford.
When Crane is headed out of New York City to Sleepy Hollow, his carriage is shown traveling on the left river bank. Crane would have to cross over to New Jersey to be on the left river bank (Western side) which he would not have done since he would have to make a major crossing to get back to the East side of the river, where Sleepy Hollow is located. Anyone traveling from NYC to Sleepy Hollow would be on the right side of the Hudson River if going North.
The village of Sleepy Hollow is located about 30 miles north of New York City. In a horse drawn carriage (traveling at an average speed of 2-3 miles per hour), it would take around 10-15 hours to complete the journey, not 2 days as stated by the Burgomaster at the beginning of the movie.
During the beginning credits, Ichabod Crane is shown traveling north from NYC to Sleepy Hollow via the west side of the Hudson River. Sleepy Hollow is located north of NYC on the east side of the Hudson River.
In 1799, Ichabod declares "The millennium is upon us. In a few months we will be living in the 19th century." The millennium - the start of a thousand calendar years - was, of course, more than 200 years away. (Also, the 19th century began in 1801, not 1800.)
The characters incorrectly refer to the Headless Horseman as the "Hess-i-an". The correct pronunciation of Hessian, which was a German mercenary from the region of Hesse who aided the British in the Revolutionary War, is "Heh-shen".