This had the possibility of being a really interesting fairy tale retelling, but it was completely overshadowed by the references to the Christian God. I don't mind a bit of religion in the books I'm reading, especially when the setting is a historical one such as this where Christianity was a staple part of society. 
 However, when the references to God are seemingly present on every other page of the narrative, it becomes too much. Weave your religion in, do it subtly, don't whack your readers over the head with it repeatedly! Doing so will only alienate readers of other religious beliefs. 
 Beyond this, the story had a tendency to waffle about things that were not of particular consequence. The villain of the piece, after having been mostly ignored for a couple of hundred pages, is suddenly reintrocued with his own PoV chapters! (This is a pet peeve of mine when authors suddenly introduce new PoVs for no good reason late in the story.) What's more, there were a number of new concepts all introduced towards the very end of the book, thus not allowing them to be explored in any detail. 
 Perhaps the biggest disappointment was how the healer profession at this time was not explored at all. With a title like The Healer's Apprentice I expected there to be more about being a healer in mediaeval Germany. As it was it barely featured at all. What a shame - that could have been so very interesting!