Infact Sanaa Lathan asked Anderson that question at the end of the commentary. It went something like this: Lathan- "I have a question from a fan, why did the Queen try and kill the Predator when it had an embryo inside it? I mean don't they sorta leave them alone while their growing?" Anderson- "Well you know how much we discussed this... em... well you can see that the Queen doesnt stab Scar in the chest, but more in the shoulder and groin area..." Lathan- "Yeah but... ok... alright..."
I guess this shows that its basically a plot hole and an excuse to have a good climactic battle at the end.