I've played 20 games so far and have seen this situation happen 2 or 3 times. Tie game, 9th inning, and the computer lets the pitcher bat.
The team had enough hitters and pitchers on the bench, so it wasn't lack of player problem. Once was a starter, once a reliever, can't remember others.
I've got Pinch Hitting set to "Often" and Pitcher Endurance is "Normal".
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