I'm guessing they hit turbulence with a shear layer which dropped them and made them yaw or bank a bit. I believe if the turbulence is severe enough the autopilot will disengage itself, which might be the cause of the autopilot rumors. It would very unlikely and rare that the autopilot caused a severe enough descent rate to cause injuries. It could cause the plane to bank suddenly and that might cause injuries, but reports say they hit the ceiling, so that doesn't seem to be what happened.
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