(at around 1h 25 mins) Later in the movie when Eleanor is trapped in her bed we can see the ceiling of her bedroom. There is a circle shaped part of the ceiling with Zodiac signs on it. But the Zodiac is wrong. There are more than 12 parts (number of Zodiac signs) on the ceiling. Also, in the first shot of ceiling some signs repeat, the order is wrong and Cancer sign is mirrored.
(at around 53 mins) As Nell and the Doctor walk into the greenhouse for the first time, we see that the man-in-the-water fountain is turned on, shooting water from his mouth. After the view changes (after the lilacs line) we see/hear that the fountain is no longer on, though there is no way to explain why it turned off.
(at around 45 mins) When Nell is sitting in the main room filling out tests, in the near shot she puts a test down, picks up a new one up, and begins to fill it out. In the wide shot, she picks the same test back up and begins to fill it out again.
From the outside, rooms have square window frames, from the inside they are arched. The ceilings, when filmed from the inside of the house, are at least 30 ft high; seen from the outside they can't be more than 15 feet.
(at around 39 mins) On the first night when the bumping sounds start Nell wakes and runs to Theo's room closing the door behind her. As Nell and Theo look toward the door the door knob is on the right side of the door. When Nell runs to lock the door after the sequence of cold breath the door knob is on the left and Nell has to push the knob to the right to lock the door.
(at around 42 mins) When Marrow asks Nell and Theo about their experience in Theo's room with the cold and the banging noises, the bag of Doritos and the bag of Lay's potato chips that are set on the table changes position between shots.
(at around 1h 18 mins) As Nell runs away and tries to hide in the carousel for the second time, the camera, in an above shot, passes behind a pillar. Just after that we see the reflection of equipment in one of the mirrors on the right side of the screen.
After the portrait of Hugh is marked up with red paint, it is said that, "Mrs. Dudley will take care of it," and the effort to remove the paint is seen later. However, Mr. and Mrs. Dudley left early on with the injured people to get help. Additionally, they locked in everyone who remained in the house from outside the gate.
(at around 1h 30 mins) When the oval from the gate falls on Nell's Gremlin, Dr. Marrow and Theo struggle to lift it from the car, but as Luke jiggles the door from the inside, one can see that the spikes are rubber, as they bend against the door.
(at around 1h 35 mins) When Luke is in the fireplace and decapitated by the fireplace flue, his body is seen lying on the floor in front of the firewood logs and on top of one of the doors in the floor when the flue drops Luke's head to the floor. After Nell says, "Oh, no," when Luke's head hits the floor, the fireplace is then shown opening its doors to spit out bones, skulls and ash. But as the doors in the floor of the fireplace open, Luke's body and head are already gone from the floor and stay gone, with only the firewood seen in the fireplace.
(at around 1h 40 mins) When Hugh Crain's spirit sends Dr. Marrow and Theo flying across the room into a wall, the wind is blowing fiercely. Theo's hair gets completely disheveled, complete with a confetti-like substance in her hair. Two to three seconds later, after the wind has stopped, her hair has no confetti in it and appears to have been brushed out.
(at around 58 mins) When Nell is reading the dead children's register, in the wide shots, the lines are not entirely crossed out (the occupation column is clean) but in the closer shots they're also crossed out.