When Leon shoots JD, he was trying to disable him in the same way he does to Sasha in the ending, as otherwise he would have went straight for JD's head. This is because JD hasn't bled from his eyes yet, indicating that the Plaga hasn't taken complete hold and there might still be a chance to save him. JD would not bleed from the eyes until after he was shot, but it seems that it was too late already.
When the Super Tyrants are taken down by fighters. It has been noted during numerous Resi media that Tyrants, while massively powerful against ground forces, they will almost always lose against vehicles, this movie proves once and for all that the "ultimate lifeform" would actually be pretty useless in a real battlefield.
Ada mentions she has no interest in "defective product" when referring to the plagas, and by her connection to Simmons and the Family, she was probably the one who gave the Russian and Americans the info that the Eastern Slav Republic government was cultivating and using B.o.Ws, as well as stealing one of their cultivated dominant plagas.
