Meet "Girl X" The love interest of my MC for my current novel tentatively called "Watchers" aka "The Awakening."

(for the record, she doesn't look like this, but I liked the expression for image sake)
Girl X, was supposed to be someone completely different than she is now. She is supposed to be nigh untouchable. She is supposed to be pristine, glass-like in her fragility, equally submissive in attitude and ultimately come across as weak. What she really is, is irrelevant. The problem I'm having is, her personality is shaping out differently. Is it detrimental to the plot, not so much, but does it bother me that I can't seem to fit my character's complex into the character... YES.
I had a similar problem with a character in Trueborn. The MC and his brother were swapping personalities and making choices that I had intended for the other to make. It feels like I'm trying to write a story about living characters who don't want to be written different than they really are. It's like they are rebelling against my finger strokes and key clicks. It's like they are developing themselves.
What is your experience with character development before and during the novel writing process?