In BAP Seasons, particularly in the reserves, I found the AI to be really dirty on World Class, constantly lunging into tackles late, hacking people down etc. There is usually about 3 or 4 yellows a game, and usually a red card every other game. There was one match where they had three red cards! They did try and patch it up a bit by sacrificing a striker and a midfielder though.
I can't say about modes where you control the whole team (I have not played many of those games) but in BAP Seasons there are loads of fouls and cards.
The refereeing is pretty bad sometimes though, others have mentioned why. I also think the offside decisions are far too prescise - your player can look level with the defender when the ball is played, but is given offside.
I think the timing of the replay is off as well - sometimes the red line (indicating the attacker) is further from the goal than the yellow line (indicating the last defender)!
There should be some margin for error in those decisions, it simply doesn't simulate real life offside decisions made by humans. I suppose no game will ever be able to replicate human decisions realistically.
