When John Gray puts the blade into the bread, it moves dramatically over the next few shots.
The scene in the pub right after it's announced that MacFarlane sold Gray's horse and buggy for a mere four pounds and the new owner is embarrassed into buying him a drink. Right after the barmaid goes to fetch him one, Fettes enters the pub to talk to the Doctor. When the barmaid returns, she has two drinks. Yet she had no indication that MacFarlane was meeting anyone, and the doctor didn't know Fettes was looking for him.
When MacFarlane and Gray gaze into the mirror and we then see their reflections in a separate shot, the partings in their hair change etc as one would expect on seeing their reflections, but Gray is now sitting on the opposite side of MacFarlane to where his reflection would actually be - i.e. Gray is sitting on MacFarlane's left so would be reflected as sitting on the right of MacFarlane reflection, not reflected still sitting to the left of MacFarlane's reflection like in the movie. The reflections were obviously filmed after a cut and the actor's swapped places in error to film that scene.
At the very beginning, they show a castle during the credits, then "In Edinburgh In 1831-" then show a closer up of the same castle and a horse and carriage, and you can clearly see two or three automobiles parked next to the castle.
The story takes place in Edinburgh, yet only Mrs McBride has a Scottish accent.
The songs are all authentically Scottish, but two of them (the ones by Lady Carolina Nairne) were not written until well after 1831, when the story is set.
Fettes says he remembered hearing his parents speak about Burke and Hare, yet the film is set in 1831 which was only two years after Burke's execution.
At 14 minutes as Donald Fettes answers the downstairs door he finds John Gray standing there with a body slung over his shoulder. As Gray carries the body into the anatomy room the shadow of the microphone can be briefly seen on the wall through the doorway.
When Gray is told MacFarlane is getting drunk in the other room, he places his whip by the door. During the conversation, the doctor makes a slight reference to the whip, but when Gray gets up to leave, he does not take the whip with him.