Is there code that jacks up the number of penalties to keep a game artificially close.

Here's the latest example. I beat my last opponent in MFN-75 by a score of 49-19, but the game wasn't that close: https://private75.myfootballnow.com/gamecenter/view/216#42198

I respect all of my opponents in 75, but my defense was completely in Mistborn's game plan.

If you look at the game log, my opponent had more first downs than I did. The reason being my team gave up 7 first downs on penalties (most of them defensive holding penalties).

I've noticed that my teams end up having a lot of penalties and that the number of penalties increases with the size of my lead in a game. Are these things merely coincidental? If so, can someone tell me how to get this coincidence to work in real life in my favor?

No, there is no code that changes anything to give a losing team any advantage in their attributes. The only thing that changes is hurry up/slow down logic which of course you have control over.