Which alignment mode are you using? It sounds like you need to scale up the set up layer. If you are using mode 1, then it only fits and scales the face to the red box. Then the bottom of the image just lands wherever based on the face scaling. If there are not enough pixels to go to the bottom then you need to setup the template so the red box is bigger. The it will scale the face larger to fit the red box and the entire image is scaled larger.
Also, for the next photo shoot, I would try to not crop off so much in camera so you have more image to work with.