Indeed, Tomlin should have a competent employee in the replay booth. Yet he obviously doesn't.
First of all, it wasn't a catch/non-catch situation. Conner got tripped up on the 5, and was twisting in the air to try and reach the goal line. He didn't know exactly where he landed, because when he lost the ball in the end zone, he quickly went to cover it. So, basically, he would have had no reason to look toward the sideline and yell at the coaches. And even in the extremely unlikely event that James had done something like that, you still would have seen none of it -- because they only showed him for a few seconds walking back to the huddle. And for the same reason, you would have no idea what Ben did or didn't do.
The bottom line is it was a bad choice for Tomlin to not challenge that play, no matter what convoluted excuses you continue to try and come up with.