IIRC, there is a time when you distribute points between 3 categories, one having to do with team discipline. I believe the other two are for recruiting and training. I think if you were to put more points into the team discipline category, you may have more in-season disciplinary points.
I could be wrong on this because:
A) I recently had a massive retro haul including a PS2 and several NCAAs. So there's a slim chance that I'm confusing it with another, but I'm fairly certain that I'm not.
or
B) I honestly didn't play '11 long, as I wasn't really a fan because of a number of other unrelated issues. So, needless to say, I don't have any prolonged dynasty experience to tell you whether or not it would make a difference.
Perhaps someone else can confirm or set the record straight.