When the couple first investigates the noise from the piano in the middle of the night, Casey Affleck is barefoot. Near the end of the movie when the scene is revisited, he's wearing socks.
At 39:04, M is in her bedroom with the Ghost standing in the doorway. As she leaves, she clearly swerves to avoid him.
At one point the ghost turns and you can clearly see the actor through the sheet, wearing a yellow T-shirt.
In the sequence of Ruth exiting the front door three times in rapid succession, the sound of the door slamming precedes the door actually closing, twice.
When the pioneer is hammering the stakes into the ground, the sound doesn't match the swing of the mallet.
When Casey Affleck is singing, the audio/video don't match up.