So I just finished Portal 2 (was awesome) but before I could I experienced a bug fighting the final boss and I figured I'd share in case it happens to someone else as there doesn't appear to be a thread about it already.
During the fight the boss is supposed to throw bombs, but when I fought him it wouldn't, or if he did they'd just hit the back of his protective shield and blow up harmlessly and nothing would happen until the timer ran out and I'd die. I did this a couple of times before suspecting something might be wrong and hit up google which led me to the fix, which is to load up your autosave from before you enter the boss' chamber and enter it again, and the problem should be fixed. Worked for me.
You'll know its the bug if his protective shields are well above his torso (they should be around his body) and he isn't throwing a steady stream of bombs around.