When Fancy Day is first introduced to the villagers and Parson Maybold, her hair style changes from a full ponytail to a half ponytail between shots.
When Fancy is playing the harmonium for the first time in the church, one shot is taken from the former choir place and you can see Dick Dewy standing close to Fancy, although he is supposed to be away.
In the final scene as the camera shows a view of the roof tops, solar panels are visible on the roofs at the right of the screen.
Just before the harmonium falters, we see the sheet music on the organ. The notated music is a completely different piece to that which is being played. This is evident in the notes on the page - no title is shown.
When Fancy is playing the harmonium alone in Parson Maybold's house, the movement of her hands fails to sync up with the sound of the harmonium.