(1:36:35) A couple passing-by on the street is seen in close-up coming up to the level of a single woman pushing a baby carriage. However in the immediately preceding long-shot the couple had already passed her by.
Capt Gregg appears next to Lucy on the train and scoffs at Fairley's motivations. The scenery going past on Gregg's side of the car is full of buildings, and billboards, right up close to the train tracks. When the focus is on Lucy, we'll see open fields, trees in the distance, farmland. This goes back and forth several times throughout the scene.
(at around 1h 15 mins) A horse who moments prior was facing the left eating grass is now facing right with its tail up, and manure can be faintly seen excreted from its rear, in perspective of Mrs. Muir's right shoulder. This happens after the ghost says "But be careful, there may be breakers ahead" and Mrs. Muir responds "I will, Daniel" and departs on the unpaved road.
Although Captain Gregg promised never to speak with Anna, he clearly breaks his word. Evidence of this can be seen as he throws the in-laws out of the house: Anna can be seen in the foreground watching without fear or confusion, thus revealing that she is aware of his presence and not scared of him.
At the beach, a man carves Anna Muir's name into a post buried in the shore and much is made of the fact that every ship passing by will see it forever. But the side of the post he carves her name in faces inland, meaning no one on a passing ship will ever see it. The name wasn't carved into both sides, either - Anna's mother Mrs. Muir has to walk around to inland side to see it.
When Lucy is talking with her sister-in-law, Eva, and her mother-in-law in her room, Eva is facing Lucy and the telescope is right behind Lucy. Captain Gregg moves behind Lucy to the telescope and then moves the telescope, rotating it 90 degrees. Eva should have noticed that the telescope turned all by itself, since Captain Gregg was not visible to them. But she doesn't react to anything.
When Coombes, the real estate agent, is discussing suitable lodgings for Mrs. Muir, he states that he took the liberty of making a list of the homes he thought would best suit her. Yet in the folder he apparently placed Gull Cottage, and every time Mrs. Muir looks at the listing, he pulls it out of her had and says words to the effect it wouldn't suit her. If he thought it didn't, then why did he put it in the folder?
As Mrs. Muir's sister-in-law and mother-in-law come down the stairs towards the ghost of Capt. Gregg, the mother-in-law has to squeeze around Rex Harrison's body to finish descending the staircase, right before he grabs the elbows of the two ladies.