The most likely reason I can think of is the way that you have your substitutions set.
Here are the following options
Let Coach Decide: Coach ignores your line-up and does what they want.
Coach Picks From Depth Chart: Coach picks who he wants based on your depth chart. Coach will chose from the Starter/Backup/Reserve at each position and play who he thinks is best.
Strictly follow Depth chart: Starters play the most, followed by backups and occasionally reserves for a minute or two. If your starter is a lot better than the backup he could play 48 minutes, but if the starter is a lot worse he would likely play less. 30-42 minutes is common in most cases.
Depth Chart Until 4th Quarter. Strictly follows until the forth and then the coach plays the guys he thinks will help win the game. NOTE: some people think that this option is broken and may not work very well but this is not necessarily a certainty.