Apparently our brain predicts where the baseball is going, and that's what we see: the prediction. In other words, we don't see reality as it actually is. Our brain performs this trick to help us survive. (After all, a huge rock falling off a cliff and heading toward you could mark your final day on Earth.)
If you'd like to learn the specifics of how this occurs, here's an article that explains it. I've written here before about how odd it is to see a slow-mo replay of a ball coming off a bat and going right for the pitcher's head. For what seems like a long moment, the pitcher isn't aware that a projectile is coming his way. That's evidence of the delay in the brain. But apparently the brain's prediction mechanism leaps ahead and alerts us (hopefully) before the ball can hit us. (J.A. Happ might shake his head upon hearing this news.)
The world is not as we see it. We see only what we need to see in order to survive. This brain trick is something that's always available to us. In fact, it's how you're able to cross a street (by predicting where the cars will be in the next 20 seconds). Are brains cool, or what? Evolution is an amazing engineer.