In the scene where the doctor comes in to look at Will's ankle, the shot changes from over the doctor's shoulder to a frontal shot of the doctor at 33:50 with his lips forming only the word "bite" when the soundtrack has the words "I don't bite" so that he has a broad toothy grin when "bite" occurs on the soundtrack.
When the Christmas tree is being delivered, the tree outside the house is very thick and full and about ten feet tall, and appears so as they are trying to jam it through the front door (09:47). When bringing it down the stairs, though, the tree trunk is much thinner and is much shorter (10:00), inferring that the bottom half of the tree was lopped off to make the scene more manageable.
In the scene where the snow comes through his window in his room in the attic at 13:42, the crow's feather is clearly covered quite a bit with snow in the close-up shot at 13:51. But when he picks it up at 13:54, there is no snow around. This is most readily seen in the full screen version.
When Will's mother is telling him about the night his brother disappeared she said she took Will downstairs and asked his dad to get Tom, but later in the movie Will's dad is telling the story and when he goes into the room Will is still in his crib.
In the scene where the Stanton family moves to the manor and the Rider is letting the ice/water run, when he gets off his horse and it is prancing behind him you can see a whip behind it making it move (from 79:10 to 79:13).