I did a run through the team penalty numbers and it appears that there is a pretty significant issue with penalties. Here is the data. It is listed by season with the highest team penalty total followed by the lowest team penalty total.
NFL2009 - 131, 69
2010 - 148, 65
2011 - 163, 76
2012 - 145, 60
2013 - 152, 69
MFN-12013 - 66, 28
2014 - 57, 23
2015 - 47, 18
2016 - 59, 19 *projected for 16 games
MFN-22013 - 55, 25
2014 - 58, 19
2015 - 61, 23
I also looked at all the season in the test league and the results were very similar. There were only a few seasons where the top team averaged over 4 penalties per game. That is 64 penalties per season.
If you look at the numbers you will see that the highest MFN teams have less than the least penalized NFL teams on average. This may explain why the rushing totals are too high for the MFN leagues. There is probably tons of holding not being flagged :) You might want to look at how intelligence and discipline factor in to how a penalty is determined.