only issue ive seen so far is certain batted balls to the shortstop are fielded cleanly, and you press the throw button, and there's a mysterious 1 or 1.5 second delay between pressing the button and the throw actually firing to first which allows the runner to easily reach first base.
i have also been able to throw 2 batters out at 1st from RF - both were catchers - with Carlos Beltran, which while pretty sweet, not sure if real-world Beltran could throw anyone out at 1B on a clean single to right.