Always!
I usually start out with a core set of characters, a world and a theme I want to explore, and a basic idea of where I want to take the plot. (In this case, the first part of the plot was already in place because of the parable I was using.) But as I'm working through these basic ideas, I often discover character motivations, ideas for sub-plots, or symbols and motifs that weren't in the original story concept.
Here are a couple of the big ones:
Joan of Arc
The boys' recurring reference in the last third of the book hit me out of nowhere! I hadn't planned a slogan or symbol or anything of the kind, but when I reached for an image for DaVonte to use in painting the improbable picture of Levi standing up to a crowd, Joan of Arc was the first that came to mind. I brushed her off and went looking for a better one. Besides the fact that she made a bit of a strange comparison, I knew she would probably never enter the mind of a tenth-grade boy.
When nothing else came to mind, I did a quick search for famous warriors. None of the names I could find had the kind of instant association I was looking for. I considered changing to a famous speaker, but that lost some of the fearless quality I had wanted. I needed something that would spring to mind quickly, but maybe I could use a more obscure reference if I related it back to their schoolwork. A quick search showed that world history was not an unusual course for tenth grade. Joan of Arc was still rattling around in my mind. So maybe use Joan of Arc and let them laugh over the silly comparison. That might work. I plugged in Joan of Arc with a quick apology and explanation and thought I was done with her.
Then Levi admired the way DaVonte had stood up to his friends. It was exactly the scene DaVonte had been trying to imagine in reverse, and the comparison was still fresh in their minds. They went back to her. Again. And again. As an example of bravery. As an acknowledgment of the possible consequences. As a symbol of their commitment. And when they crossed swords with fish sticks to cement their bond (another completely unplanned moment), I had created what may well be the strangest secret signal in the world and given myself one of the most unexpected moments in my own writing history.
Asher and Natalie
For the first two thirds of the book, these two were my most unexpected treat. In the very early planning stage, they hadn't even existed, and they were added entirely for practical reasons--Natalie to illustrate Peyton's total self-absorption and Asher to ask questions and carry on conversations that Levi would have let drop.
Because of the distant point of view I had chosen, dialogue was key to Levi's and Peyton's scenes, which meant it made sense to continue using them, but I never expected to love them as much (Asher) or give them as significant a role (Natalie) as ended up happening.