Continuity mistake: In the scene where Mary is eating her oatmeal while Martha is talking to her, take a look at Martha. While talking to Mary she spits out a piece of bread she was eating and this causes the little girl who plays Mary to momentarily slip out of character and smile (almost ready to laugh).
Continuity mistake: When Mary leaves the house to play in the garden, her hair is untied. However, a few shots later we see her exploring the grounds of the house, and her hair is now in pigtails.
Continuity mistake: When Dickens is feeding a newly born lamb a bottle of milk, half way through, the bottle gets smaller and filled with more milk.
Continuity mistake: When we first see the lock to the secret garden the keyhole is to the right of the handle, but later the keyhole is to the left of the handle.