setting target and max pitch counts too high could be contributing. take a look at the IP/G stat for your pitchers, that's what determines how quickly pitchers fatigue during a game. a good general rule is 15 pitches per inning (a bit higher for high BB, high K pitchers and a bit lower for low BB, low K pitchers).
so if you have a reliever with an IP/G of 0.9, setting his pitch count any higher than 10/10 will lead to trouble. if you have a starter with an IP/G of 5.5, don't have him any higher than 75/80.
also, check the use in relief box for your starting pitchers! this is probably the biggest mistake people make on the site. if you don't check this, the sim will use fatigued relievers before using a 100% starter and your bullpen will be blown out.