Yeah, i certainly know i've gone at Combine before, using barrels, or trash cans as shields, let alone a medicine bottle, and i got shot several times. I've never seen the AI act quite like that, it always seemed much more intelligent.
The hitboxes are a bit annoying and yes that's a flaw, it might be because the hitboxes are rectangular, and since the models are in a semi crouched position, the hitbox extends over that shoulder. They repeatedly showed these same two flaws, which only goes to prove that there really wasn't anything else wrong with it.
The only one which i find more of a problem was the door blocking one....he piled a lot of **** on that door, a soldier shouldn't have been able to push it open. but, all games do have flaws, and this is one of HL2's.