Question: Why can't Henry save his mother from being in the car crash? Couldn't he have warned her when they met on the subway?
Answer: Of course not. Why would she listen to him? He's a total stranger. And if he tells her he's her time-travelling son, she'll think he's a nutjob to boot. It's well-established in the book that he tried everything to save her but could never do so, which made him recognise a well-accepted convention of time-travelling lore: big past events can never be changed. Diana Gabaldon wrote an excellent and extensive essay on time-travelling laws, which is probably still available somewhere on the Internet.
Question: Henry gets shot and when he time travels, he dies in Clare's arms. Years later, Henry appears to both Clare and Alba. So is he still time traveling or is he really dead?
Answer: He's really dead. But while he was alive, he time-traveled far into the future and saw Clare and Alba. His "individual timeline" is scattered, out of chronological order, all over the "real timeline, " so he can appear in the "future" as a younger (or, in this case, living) person.
Question: There's a scene in which, right after they've bought their house, Henry appears in their living room, naked and shot. I just don't see how this can happen because this would constitute a travel within a travel. That is, he travels to where he gets shot. Shot, he then travels to the newly-bought house; then finally travels back to the Christmas party from whence he came originally, where he finally dies. But the movie never establishes this sort of "Inception"-like travel. He always travels to one time, then comes back. Is this something that the book clarifies, or is it a mistake from the movie?
Question: At the end, Henry goes back to the meadow. Alba is there, now 9 yrs old, and the Gomez kids are there also. Henry says that they've gotten so big. Alba sends them to go tell Claire that he's back, but Claire is young again, so how are Gomez's kids there? Alba and Henry time travel yes, but Claire is young again, so how are the other kids there as well? I'm confused or just not seeing it right.
Answer: Not sure what you mean by Claire being "young again." Henry dies when Alba is five years old. His younger time-traveling self reappears when she is nine, so that is only four years later. Claire would barely have aged in that short amount of time. The young Gomez children, however, would have grown quite a bit in four years.
Question: If Henry time travels and his clothes are always gone... why doesn't this happen to his daughter Alba?.. Or if Alba can time travel wouldn't they worry if she did as a baby and be helpless when she reappears?
Answer: If the fetus could travel then there would be no age limitations on time travel.
Answer: Alba's clothes DO disappear. The first time we meet the slightly older Alba she is playing outside with her younger self. Henry notes that she is barefoot and wearing a too big, old T-shirt - maybe a shirt young Alba found for her.
Answer: It was never explained why Alba's clothes did not disappear. It's one of a number of inconsistencies that occur in the movie's time-travel plot. Most likely it had to do with the legal and ethical issues of child nudity in a film, which could potentially violate child pornography laws or allow unscrupulous third parties to exploit the images for pornographic purposes. Also, Alba may not have been physically able to time travel until she had grown older. Of course her parents would worry if she did, but they would have no control over it.
Answer: He could have had Claire distract her long enough to delay her car ride and miss the accident.