Found a serious problem during my most recent game. (Or, more accurately, confirmed something I'd suspected for a while.) I was running trials to determine if I could use multi-stage missiles to exploit the same loophole that ships firing missiles at very close range do. The answer turned out to be no. However, as a control, I first fired the same missiles I was using as second stage from long range. (They were my standard second stage for this game, just set to go off much closer.) The hit chances of the defending ship were exactly the same in both cases. I've noticed the effect before, and not been sure if it was real, but I'm sure now. I have tracking bonus 80%, and the first case should have had a 22% tracking bonus, while the second should have been 0%.
It's possible that this was fixed in a later version, but I don't remember seeing it in the change logs. If it was, I apologize.