When a pitcher gets a key hit, it stands out and without doing any analysis it seems they get more hits than they should. Any examination of stats shows that is not the case. It's like an A+ SS making an error in a big spot, which stands out more than a C- SS making a few errors over a few games. You need to realize that a pitcher with a lousy .050 average is still going to get hits once every 20 at bats, a third of those will come with two outs, and some will drive in runs that win games. There's a big difference between rarely hitting and never hitting, and the difference seems exaggerated when playing live games.
I checked pitchers' batting averages for all my teams that are more than a third into their seasons (including only pitchers 50+ PA in real life):
• 8 are hitting better than their real-life stats, 7 are hitting worse.
• 7 of the 15 are within seven points of their RL average; statistically, that's hitting exactly what they should.
Looking at your two teams well into their seasons likeastone, your pitchers with the most RL at-bats on one team are hitting .195, compared to their RL averages of .206; on the other team, they are hitting .086 compared to .132 in real life. If someone were to take the time to compute the difference for all the pitchers in that league, I'd wager that the diffrerence between RL hitting and sim hitting is close to non-existent.