I find that the AI does the same exact thing. I have played maybe 10-15 games in Exhibition while waiting for the v2 Rosters and I seem to throw a guy out at home every other game.
Most of the time it's not even close and my Catcher will get the ball while they are only about 2/3 down the 3rd base line. It is always followed by the "he ran through the stop sign" dialogue.
Seems to be another thing that needs to be fixed with the AI. I wouldn't doubt that making the AI more aggressive for stealing is part of the problem and it's spilling over making them too aggressive while rounding the bases.