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.
Continuity mistake: Walter near the beginning of the film, is going over the ship's systems. He checks the fetuses inside a compartment and sees a dead one. As he removes it, the slot it came from is full of blood. He places it inside a container. Then as he hits the button to close the compartment, the slot has no blood in the next shot, and no implying he cleaned or decontaminated the slot.
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.
Continuity mistake: Daniels' face gets splattered with blood but when she uses the radio to call back the others, her face on the screen shows no blood. In the other shots after it's there again.