When I see odd things with the 3D play I just check the play results to see what happened. They're limited in how many grounders to 1b who throws to the pitcher or two out grounders to 3b who throws to first instead of going to the bag graphics they've got to display the action on the field. Would be nice if they had dozens to display each possible play but even then eventually the program would make an odd choice that we'd take note of because it clearly struck us as weird.
btw, I play out all my games, sometimes on one pitch and sometimes pitch by pitch. Depends on how much time I have and how I feel. Gotta play 'em out to get packs in challenge mode.