When the children are in the attic Emma is holding the tray of cookies. The cookies disappear when the children "must hide" and reappear in the hiding spot. There is an extended scene on the DVD that explains how the cookies appeared there.
When the Evers family is driving to the mansion, Sara is wearing a bright yellow suit. When they get out of the car, Sara's suit is pink, and it is yellow again when they enter the mansion.
When Jim's daughter is coming out of the water in the crypt after getting the key, a hand with a glove and a watch grabs her shoulder. It turns out to be Jim. However, in several shots before and after that, his hands are bare.
When Ramsley throws Jim out of the mansion, the ground Jim lands on is dry though there had been a flood earlier that same day.
When Jim and his daughter are trying to get out of the mausoleum you can see that from the inside the door that light is showing through the cracks before Michael opens the door.
The Evers' car has a personalized Louisiana license plate on both sides. Louisiana does not issue front license plates.
The large columbarium (mausoleum for crematory urns) in the Gracey cemetery could not have existed because the first legal cremation in the United States did not take place until 1876, and the practice did not become common until the 1890s - long after the circa-1855 Gracey backstory.
After Jim exits the painting and goes into the hallway, look down onto the rug. You'll notice dark lines on them, that's not part of the rug as they tried to make it look, it's the railings for the ride. They filmed it inside the ride, that includes the rails leading to the breathing door.
When Jim Evers finds the letter in the trunk, and the camera is shooting upwards at him from the POV of the trunk, a modern day spotlight is visible to audience left, hanging down from the ceiling.
There is no obvious reason why medieval European characters, including an armored knight, a king, and a queen, would somehow be buried in a private family cemetery in 19th-century Louisiana.
A few jokes are made regarding Madame Leota's inability to move on her own. However, when Jim Evers is trapped outside the house (after being thrown from the attic) she seems to have the ability to roll along under her own steam. Of course, this is ignoring the fact that she'd need to be able to get out of the attic in the first place.
The term for killing one's self by a rope around one's neck is "hanged" not "hung."
Ramsley tells Jim that Mr. Gracie would like to meet with him "in the libary", a mispronunciation that someone of Ramsley's pedigree and impeccable enunciation would never make.