I'm kinda surprised that you of all people brought this to our attention, C&SD. You're normally "johnny law can do no wrong" when it comes to LEO snafus. I thought of posting this to APS when I heard about it yesterday, and imagined your response would be rather different than mine.
As far as the story itself goes.... Mom says they were at church when the calls went out.
Either the kid VPN'ed into his own router from church then launched a VoIP call, the kid wasn't at church with his family, or someone else got into his router.
Interesting they arrested the kid though... and not Mom or anyone else. That they deliberately went after the minor in the house rather than the legally culpable party. Makes me wonder if they have audio that matches his voice. Or something else that points to the kid in a more direct manner than a router IP address (which is pretty weak evidence, IMO).