Looking at your images, and the fox one in particular, it looks as though the main cause of the depth disruption is the strength of the light source and reflections from glossy / metal surfaces. When there is a very strong light source like the one behind your fox, the camera's IR emitter component (a component that aids the IR sensor with exposure) can get saturated and cause those large black areas.
The cameras have trouble coping with reflective surfaces at the best of times, but a strong light source casting onto them will increase this problem further, as evident by how the metal stool is a bunch of black lines.
Your options for improving the image include:
1. Turn off the IR emitter component with scripting.
2. Move your scanning location to a place where the light source is not as strong and there are less reflective surfaces around the object being scanned.