I've been noticing this with 3.6. Here is one of the most glaring examples:
In the first mission of "Just another day", when that Cain appears off the side of the Sasquatch, the Sas fires it's side Terslash, totally missing the Cain. It missed every single time, and appeared to have missed by exactly the same distance every time.
Another example was in Derelict:
In that mission where you have to fly within a certain distance of 3 Shivan cruisers and then let the Ignatius blow them straight to hell. At least in theory. In reality, it's first beam salvo only occationally hits them. During that entire "battle", the Ignatius' beams at best just nick the cruisers. I have seen this happen every once in a while.
This is the kind of thing I'm talking about. I've also seen numerous other examples of this too.