Agreed that you need to check your pitch counts. Make sure your starters' stamina is at least 60. The pitch counts I generally use are: stamina 60-69 (90-100 pitches), stamina 70-79 (100-110), stamina 80 and above (110-120). Again, that is a generalization. Also, what is the Call Bullpen setting at? In the minors, I will put all pitchers at 3. This is middle of the road. 1 means they will get left in games longer, 5 means the quickest of hooks.
Also, I generally have inactive pitchers I swap into active roles depending on which relievers are fatigued. AAA = 1 or 2 extra pitchers, AA = 2 or 3, HIgh A 3 or 4, Low A 4 or 5. Rookie you have room for tons of pitchers (I'm usually at at least 16 of the 30-man roster). I usually do the reliever swap twice a day when I check in on my teams.