When Coraline first looks at the picture frame next to her bed, the "3" from "at 7:30" is missing and "Coraline" is spelled "Coral1n3" on the depicted sign. In the next shot, when she holds the frame in her hands, it says "7:30" and "Coral1ne".
Coraline's puppet has its legs extremely thin in the beginning of the movie, but when Coraline goes to Bobinsky's house to deliver his cheese the puppet's legs are thick and apparently "normal".
When Coraline first meets the Other Father in the study and is playing his piano, he sings Coraline a song. Notice the red record player in the background is facing Coraline. But when he sings "She's a doll", it is now facing the wall.
When Other Father starts playing the piano, the piano gloves go on his hands while he is facing Coraline. After he turns around, the gloves switch hands.
When Coraline falls asleep on the picture frame, at first it is facing down, but when the shot changes it has flipped to facing up.
Right before Coraline discovers the door, she drops her notebook, and just in one screen shot you can see the wires holding it up.
When Coraline first meets Other Father, after Coraline tells him that the dinner is ready, he raises his hands in the air and the bottom of the puppet's neck clearly comes apart for a second.
(at around 52 mins) During the Other Forcible's trapeze act when she says "In action like an angel" the lines where the puppet's head comes apart are clearly visible.
Where Wybie asks Coraline to take his photo, and then hands her his camera, a flash goes off but there is no flash attached to the camera and the Leica M3 has no built in flash.
Watch very closely during the opening as the hands unstuff the doll, and restuff it. When you see the doll inside out in full, look down at her feet, with the heel stitches on the same side of the body as the face.
When the Other Father is sadly playing one key on the piano, the sound is F#, when the key he's pressing on is actually F.
The house's living room changes places several times throughout the film.
Mr. Bobinsky is Russian, but the flag in front of his door is Montenegran, with one minor difference: The real one has a lion passant in the centre, while Mr. Bobinsky's has a horseman.