You will mainly get 3 penalties. False start, offsides, and roughing the passer. I got a PI call when I threw to WR in press coverage. With similar settings I was in the bottom 3rd of the league for most penalties. You need to develop some sort of house rule for fake snaps. I usually just go with a feel or if the CPU defense gets a penalty.
You will get offsides and false start penalties. I know no other way to get realistic penalties in M24. I average 4-6 per game and the CPU does the same. And the penalties feel right. It sucks when you stop a team on 3rd and long but they get a first down because you got a defensive penalty (roughing). But that's football. If you want no penalties turn down roughing and don't fake snap.