A few things here in my estimation...
First, Fish is too nice to the refs, so they don't fear making bad calls vs his team. It is something he needs to quit doing, that "I'm a competition committee member so need to take the high road" BS.
Second, I think the rules are just too complicated. It's to the point where the refs have too much heaped upon them, and they're only human. Every year the NFL changes the rules around and seems like they add more and more to the pile refs need to manage, what with concerns over player safety and whatnot.
Third, the desire is to have this be a passing league. The rules are being adjusted to get there, IMO. So the Rams would do well to see that coming and take advantage.