My personal theory on why he stuffed up so badly is that he was so keen to play KR's voicemails for that time period to the jury that in his excitement he overlooked or failed to register that his witness would make a note of where the phone actaully was when they were sent.
Possible. Let's face it, he had to play them for motive, weak as they are with regard to that.
Or he just relied on Jen McCabe. An obvious liar.
None of the seven calls Jen made were butt dials. They never went to John's VM so she made them, hung up, and did it again. Why? And why the texts around the same time? She and Matt were looking out the dining room window. Maybe not the whole time but if you're looking for someone to get out of a car and they didn't respond to your 12:31 contact, wouldn't you glance out to the street before sending a barrage of calls and texts their way? Karen had to have been gone before 12:31.
I don't think the defense is going to bother calling Erin Beatty (although she's on their list) as they think the case is already won, but she told an investigator Colin contacted her around 12:30 for a ride. Despite literally everyone else remembering he left at exactly 12:15 (not that they remember much else) and despite the McCabe daughter's very questionable testimony. (Life360)
My speculative timeline is that John got out of the car immediately and just before the three witnesses noticed Karen alone in her car. He was in the house by 12:24 or 12:25. Not hearing back from him, an upset Karen heads for home at about 12:29. The CW says the GPS on his phone stopped at 12:25 (By which time I think he'd arrived inside the house) but his health app time stamp has his phone moving until 12:31.
I think he was smacked in the head with a hard object and disabled shortly after he arrived, with Chloe getting involved at some point. Instead of calling 911, Colin is hustled out and Jen tries to muddy the timeline waters with all of her calls and texts pretending she doesn't know where John is. A drunk Higgins heads out to Canton PD to establish an alibi. Despite the fact that he returned to his home (10 miles away) earlier to prepare to work, Tristan Morris, Caitlin Albert's fiancé, is called back to Canton to help and get Caitlin and possibly Chloe out of the house. After Lucky's first pass around 2:45 am (when there is no body seen on the lawn) BA and Tristian move John's body to the darkest part of the lawn, using the SUV Lucky saw as cover from the street.
BA knew full well he could count on his cop friends not to ask any actual questions. And he was right.
Just my speculation, of course.