Pitchers Batting

What's up with the pitcher hitting and not being pinch hit for.
I'll admit, I usually play DH leagues, so this doesn't happen, But here's 2 games where the pitcher batted and I don't see why
This one, bottom of the 7th, 2 on 2 out, scored tied at 1, relief pitchers bats
http://onlinegames.strat-o-matic.com/game/349464/871

This one is far worse: Bottom of the 6th, 2 on 2 out, 4-1 game, pitcher bats, then HAL relieves him in the top of the inning
http://onlinegames.strat-o-matic.com/game/349464/877

Any idea on what's going on, this is craziness?

Depending on the whole situation (RPs fatigue, L/R coming up next inning, etc), the first situation might be defendable. The second drives me nuts - a scoring situation, pitcher hits and then gets yanked. In the first five innings - maybe. 6-9 - never should happen.