Who was watching Mary in her childhood? After the credits there is a final flashback of Mary and Charlotte when they were children , they talk about the Shadow Builder and how he hates humans because "when God said 'Let there be light' he went away", Charlotte worries about the existence of the Shadow Builder for Mary's safety, yet Mary reaffirms that she'll be ok and will protect Charlotte saying that since that the Shadow Builder can understand her because he listen to god.

At the end of the scene, Charlotte notices in Mary's shadow a red eye, the same kind of eye which is depicted though the entire story being associated with Sharnoth, this eye however is just watching and it has no red tear.

I am wondering who this eye represented and what reason did they have as she did not have her Golden Eye at this time.
The eye was James. Hence the part where it says the "red eye warped/as if looking at something bright" hearkening back to the many times it mentions James doing the same.