My speculation about the phone:
Ashley or Paul gave Noah their WORKING phone before leaving that morning and showed him how to call someone if their was emergency while they were gone (presumably how to call the other parents phone). Unfortunately something did happen while they were gone but Noah probably couldnt call because he was either unconscious or deceased. Ashley comes home to find him incapacitated in some way. She panics and is worried about getting in trouble. With adrenalin coursing thru her veins, she picks him up and decides on the septic tank. She prays no one sees her. Once she has dumped him in there, she realizes she cant find the phone. Once she decides to report Noah missing, she realizes she cant report the phone missing because somebody will ping it and not only will they know where the phone is, but also her childs body.
As for how this helps the defense, she has already admitted to leaving him home alone, so now she can say, "see? We gave him a way to reach out in an emergency." Plus, she can argue that if she disposed of her childs body, why would she leave her phone with him when its traceable, so therefore, this was just a horrible accident that happened while she drove Paul to work.
I believe the first part happened but not how the defense may use it.