Why is Clara having such a hard time adjusting to the Doctor's regeneration, she's saw all his incarnation in "The Name of the Doctor"?
Well, she understood the concept of regeneration, but that's not to say she accepted it or was okay with it happening—we're very much in "Some new man goes sauntering away" territory here, it's just that it's the companion rather than the Doctor who can't help but think of the regeneration as a death. Especially given the stark contrast. If Eleven had regenerated into someone more like, say, Ten, she likely wouldn't have such a rough time of it, but instead he became someone who (as we can see quite quickly) is a darker, less personable Doctor. ~Celi
Oh, and Clara didn't see the Doctor's future incarnations—at that time, the Doctor was fated to die on Trenzalore.
We're talking the woman who went through his entire time stream and saw every iteration of the doctor that has existed thus far, who personally MET nine, ten, and ten 1/2, and who has had the whole regeneration thing explained to her multiple times. She should be the LAST person shocked by this. I'd understand it as a panic-in-the-moment kind of thing until she gets used to the new doctor, but even at the end she's treating him like a completely different person who she doesn't like or trust until she gets the phone-call from 11.
She wasn't shocked by the regeneration exactly it was because she fancied him, no matter what she might say, and was overreacting because of it (and Eleven fancied her too judging by his comments.) Everyone always tries and takes the high ground in these kinds of situations but be honest, if your boyfriend/girlfriend suddenly and visibly aged 30-40 years wouldn't you be on the verge of breaking? Like it or not love is always half physical. Or to put it another way: Imagine if Tennent regenerated into Eccleston; would Rose have still fancied him? She certainly shows no sign of it beforehand.
The above is basically it; it's not the regeneration itself that upset her, it's the fact that this man she thought she knew is now completely different. Even removing the shipping aspect, if someone you knew well and were incredibly close to suddenly became an entirely different person, it would throw you a bit no matter how much you were intellectually prepared for it. There's a difference between having knowledge of something and experiencing it directly firsthand.
Moreover, she'd only just seen Eleven aged nearly to death, and honestly believed until the very last minute that he was going to die permanently in "Time of the Doctor". For one brief conversation, she sees him young and well again, only for him to change again into a visibly-aged man. On some level, she'd already equated the Doctor becoming old with the Doctor being gone forever.
She also saw the First, the original form of the Doctor, and an old man (older than any other version other than the dying Eleventh). In fact, she has seen all of his 2000 years of life, by jumping into his timestream. Grieving over the "death" of Eleven would be fine, but her reaction is completely incoherent with what she has gone through in a very basic level, and this annoyed me greatly too. This episode would've made much more sense with Amy as a companion (even if it would remove the "boyfriend" thing), as she is the one who is familiar with only Eleven being the Doctor.
It was established in "The Day of the Doctor" that Clara only remembers "a bit" of her time in the timestream; apparently not even enough to recognize the Tenth or War Doctors on sight. In this case, it was kind of a combination of two things. 1) Even though she understood that he could regenerate, she had not experienced a regeneration first-hand. I understand that somebody could break into my house and try to rob me, but that doesn't mean that I would automatically know how to react in such a situation. When she met War and Ten, it wasn't for a terribly long time, and she made it clear then that they weren't "her" Doctor. She had no ties to them, because she effectively saw them as different people (not that one could blame her; seeing the Doctor interact with two strangers who look and act differently would give one the perception that he was interacting with two strangers who look and act differently, not literal copies of himself). She may be consciously aware of the fact that they are his past, but that's just it - they're the past. He has changed since then into the person that she has become attached to. She may not know about post-regenerative trauma and may not know why he was acting like he was. Plus, she had just been with him on Trenzalore when he told her that he once regenerated and kept the same face, and then she later saw that for herself when he regenerated on the clock tower but came out looking like... Matt Smith. So it's possible that he didn't know that those were unusual circumstances. And moreover, 2) she understood the concept of regeneration, but what threw her for a real loop was the fact that he got older. As I said, she's never experienced a regeneration first-hand. What reason would she have to think that he should go from young to old if he's being "renewed"? She saw War, yes, but she knew that he'd been in a high-stress war zone for his entire life and may have (correctly) assumed that he started out looking younger. In this case, she had just seen Eleven age tremendously over the time on Trenzalore, and she clearly didn't understand why he was starting out aged here. So there are a lot of factors present that could contribute to her mindset in this episode.
So the robots were the same kind as those aboard the spaceship in The Girl in the Fireplace? But in that episode the robots went crazy and started replacing the spaceship parts with human parts only because they were stranded in space, and had nothing else to use. However, the robots in this episode would have had all the inorganic raw materials they need, yet harvesting organs now seems to be their default mode? Does not compute.
You can't say the robots on the SS Madame de Pompadour had nothing but human parts to use, at least not by the time of the episode. The spatio-temporal hyperlinks gave them at least as much access to raw materials as the SS Marie Antoinette had but they still insisted on using people—or at least Reinette—for the repairs.
Okay, but if that's true, the question still remains: why were this robots programmed to use parts taken from living humans to repair things? If it had only happened with the robots of Madame de Pompadour, you could brush it off as a malfunction, but since the same happened with this other set of robots too, it seems to part of their basic programming. However they were built and programmed by humans to help humans, so why introduce an element to their programming that can cause them to kill humans?
We don't know how widespread that bug was. All we can say is that it turned up on two sister ships (specifically noted in this episode it is the Pompadour's sister ship) that had the same type of accident. For all we know those ships were purpose built, using the same code, and sent off together to explore strange new worlds and boldly split infinitives. Then they ran into a temporal anomaly, and the robots (for reasons of sloppy coding; good old GIGO) both defaulted to the same technique. It is entirely possible that this bug existed only on these two ships because they were paired.
For that matter, it's possible that the two ships were traveling in convoy when whatever mishap that disabled the Pompadour occurred. A control Droid on one of the ships suffered a malfunction that told it to using organic materials for repairs, and passed this instruction on to its counterpart on the other vessel. Both ships' crews were broken down for parts, but it wasn't enough to restore the vessels. The Marie attempted a time-jump to acquire the needed material for both ships, but crashed upon its arrival on Mesozoic Earth. The Pompadour's Droids, seeing that their sister ship hadn't come back, tried using time-windows instead of jumping their whole vessel into the past.
Why was it left ambiguous whether or not the Doctor killed the cyborg guy? The Doctor doesn't have a "no killing" code like Superman, we've seen numerous times that he's perfectly willing to kill when necessary. And in this case he was fighting for his life (as well as the lives of his friends, if he realized stopping the head cyborg would stop the others). So why is it all of a sudden ambiguous whether or not he's a killer?