At the end of The Prodigy, Edward Scarka (in Miles's body) says that his soul had taken over Miles's since the night he said to the mom "will you always love me, no matter what I do" (I might have misquoted that a tad), and that Miles had been gone since then. However, when Miles/Edward met with the spiritual guy, Miles did scratch Scarka into the couch, showing that he actually hadn't been gone by that point, and the meeting with the spiritual guy was after the night the mom said she would always love Miles.
So does this potentially mean that at the end of the movie she was about to shoot a body containing her actual son's soul? I wouldn't think so, since the movie did make it seem like Edward's soul had completely taken over and rid of Miles's, but then again, that lie above I just mentioned makes me think Miles could have still been there (why else would Edward lie).