all short passes
 

I have noticed one thing in my games is that teams that throw a ton of screen - short passes kill me.

I play a huge amount of my base defenses as 2 deep.

Any ideas on how I can correct getting killed on the short and screen passes?

In real football you would stop them by using more bump&run defenses and less blitzing, but i have not tested if it translates well to FOF. Check if you are blitzing a lot, if the other team is good blocking your blitzes or reading them, short routes will get open for them in the areas left empty by the blitzing players.