What he didn't know though is that Walter was able to regenerate skin when injured, so when he was stapling his face back together again, she figured out that it was David, (so why she then got into her sleep capsule is one huge mystery).
As we don't know whether Walter is now in a state beyond repair or in the process of regenerating whatever damage David inflicted upon him, it is possible we may see him again if he can get off the planet.
Actually, she did not know he was David until she was in the capsule and asked him to help her build her cabin. When he didn't have a reaction, but looked blank, then she knew it wasn't Walter.
I don't know if it was intentional or not but I got the impression she had her doubts about him, it wasn't left to be very ambiguous to the viewer so I'd have thought there might be a confrontation between them.
When she actually started getting into the pod I became extremely irritated that she actually trusted him, especially considering I had the impression she doubted he was Walter. After all she had been through I wouldn't have thought she'd take such an apocalyptic risk. As I said, it was just irritating to watch, partly due to its sheer predictability.
I don't know if it was intentional or not but I got the impression she had her doubts about him, it wasn't left to be very ambiguous to the viewer so I'd have thought there might be a confrontation between them.
If I remember correctly she had her doubts earlier but when david/walter assisted them in killing the xenomorph she trusted him. Yea we were all thinking it too but meh.
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I became extremely irritated that she actually trusted him
Characters doing dumb things that defied all logic were the driving force behind movie. See: Captain Oram sticking his face into a freshly hatched egg.
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That's the reaction I got too. She didn't know until the "We'll build a cabin" moment. Up until that point she was all smiles too.
I guess she also wasn't aware of Walter's ability to regenerate Perhaps she never really saw him injured so she naturally assumed David was Walter, and that those injuries on his face were normal for androids.
This really annoyed me. It was obvious from the way they cut away from Walter about to punch David (therefore not showing what actually happened) and then 'Walter' was suddenly on the ship and despite having been shown minutes earlier that he can regenerate injuries (on his head and neck at least) we see that this 'Walter' has injuries on his face, making it obvious it was actually David, which begged the interesting question - what happened?
Walter had the upper hand, was about to smash David's face to a pulp, he was the newer, stronger, regenerating model, so how did David defeat him and take his place? Given that the last thing David says to Walter was 'are you going to choose them over me, serve in heaven or reign in hell' type thing, it made it seem like Walter had chosen to go along with David's plan or had let David take off with the ship or something, or had sat around to ponder his options long enough to let David reverse the situation. Which would have been a interesting decision/character development for Walter worth seeing. Really annoying as it seemed to take some interesting themes and ideas about AI's relationship to humans, creatures' relationships with their creators, consciousness, love, hate, good and evil, that were kind of expressed a little in David's ramblings, and then just ignored all that for an obvious, trite, tired, cliche plot twisty evil-good guy switcheroo. Annoying.
I think she did have her doubts about 'Walter' on the ship when she offered to help staple his face, he then moved to make it obvious that he had lost the hand, couple that with the fact that David was now talking with an American accent, instead of his original English accent, she seemed to accept it was actually Walter.
When she mentioned the cabin while in the hyper-sleep capsule, and he stared blankly back, I got the impression that she then realised that her original suspicions were correct.