Plot hole: The computer on board the ship mistakes David for Walter. This makes no sense as while a human being could be fooled by his appearance or his voice, a computer with detailed sensors and possessing the exact details of David's composition would not be fooled simply because the two "look" and "sound" alike. In fact, Walter, being a newer and more advanced model, should be composed of different chemicals and materials than the earlier manufactured David making it even less likely that the ship's computer would have mistaken the two.
Plot hole: At the end David regurgitate's the alien embryos and places them in the refrigerator with the human embryos, thing is they are in exactly the same matching capsules as the human embryos and are an exact match for the compartments and fit perfectly. Impossible as he would have no idea of the refrigerated compartments or the layout of the ship.