This wasn't a judgement call. Based on NFL rules, the refs called it 100% correctly - anyone who understands the rules agrees with it. There is no "the refs messed the call".
A lot of people have brought up the runner argument but when the runner is running into the end zone, he has already established possession way in advance even before reaching the goal line so anything after crossing the goal line is irrelevant because the plane was broken with possession. With Jesse James, he caught the ball and fell forward at the same time - clearly one action, easy call for incompletion.
The NFL is such a quick game where every play is bang/bang, the NFL's catch rule makes sense. Let's imagine that Jesse James made the catch and got hit hard and lost control, how many people would be crying incomplete pass and no fumble? If this catch rule didn't exist, the number of fumbles would sky rocket.