Jasper tries to get away from Arcadia in the rover, which was previously described as completely solar powered, i.e. electric. When Jasper drives through the gate, the rover stalls, which is something that can happen to a combustible engine but not an electric-powered engine.
At the end of the episode when John Murphy was put in a iron collar it was not locked completely.
It was previously stated that the AI chip interrupted or otherwise blocked the brain pathways that process things like pain and thought. If the chip could control or limit the brain's pathways, the anesthetic to render Raven unconscious would not have worked.
When Jaha was under the control of ALIE, he could not have suggested to ALIE to override freewill because voluntary consent of subject was paramount for ALIE to proceed. A subject, in this case, Jaha, could not have overridden the hardcoded programming of ALIE. Raven could have, as she was strong, but not Jaha as he was not as strong as Raven.