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.
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.
When Theo is first introduced to her bedroom in the mansion, she jumps onto the bed with a somersault, placing her feet onto the pillows. But in the subsequent shot or that scene, it shows her lying on the bed with her head on the pillows.
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.
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.
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.
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.
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.
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.