
Question: How come Harry and Peter stopped living together?
Answer: While it's never mentioned in the film, the most likely explanation is that Harry, as a rich kid, grew tired of "slumming it" and decided to move back into his mansion.

Question: Given that Logan's body (skin, bone, muscle, etc) is what "regenerates" quickly, and Adamantium is absolutely fixed once it is solidified, Logan would now have two permanent holes in the front of his skull from the bullets fired into his brain to destroy his memories at the end of the film? Unlike the skin, muscle, bone and brain tissue, the Adamantium would not "heal over" or regenerate, so the two vulnerable bits of bone would remain, a bit of a vital vulnerability in a dangerous area of the body.
Answer: That would indeed seem to be the case. Granted, it would have to be an extremely lucky shot to find one of those holes under his flesh, but, yes, it is an apparent vulnerability.

Question: Whenever Tim goes back in time, his clothes change to whatever he was wearing at the time, but he always appears in the same spot that he left from. Both times he goes back to the NYE party he appears in the upstairs wardrobe. So what happened to the version of him that was already walking around at the party? Did that version of him just vanish?
Answer: This is one of the (many) time travel plot holes in the film, and unfortunately your question doesn't really have a definitive, or satisfying, answer. Richard Curtis has said he was less concerned with making an airtight time travel film than with the human story at its core, so he let things like this slide without explanation. However, since we don't see any "second" Tims around when he goes back in time, and no-one else seems to think of him as an "extra" Tim, we can safely assume that, yes, he replaces himself in the timeline when he travels back. (Of course, this doesn't explain what happens when he then returns FROM the past).

Question: I heard that the marble ashtray that Bedelia uses to kill her father Nathan in the "Father's Day" segment appears in all the stories. Does anyone know the specific scenes it shows up in in the other ones?
Answer: Besides being in "Father's Day", it showed up in "The Lonesome Death Of Jordy Verrill" right next to the cash box at the Department of Meteors. In "Something To Tide You Over" on the nightstand next to Richard's bed. In "The Crate", it was on the writing desk when Henry writes the letter to Wilma. In "They're Creeping Up On You", Upson Pratt uses it as a soap dish. And in the epilogue, it appears on Billy's desk when he starts stabbing the voodoo doll.

Question: I'm aware that there is debate on whether or not Deckard was a replicant, but as I was watching the movie, I couldn't see any clues as to why anybody would think this. Did I miss something obvious? Why do people think this?
Answer: The two most notable hints are as follows. The first (which is only in the Director's Cut) is that after Deckard dreams of a unicorn, Graf makes an origami unicorn and leaves it at Deckard's apartment. Some people interpret this as suggesting that they're aware of the memories that have been given to Deckard to prevent him realising his true nature. The second hint is that replicant eyes glow in certain lights - at one point in the film, Deckard's eyes can be seen glowing in the same fashion. Ridley Scott has stated on several occasions that, as far as he's concerned, Deckard is a replicant, but he does concede that they deliberately left it as somewhat ambiguous - the viewer should decide for themselves.
Answer: In addition, if it counts, in the original version of the movie, Bryant says there were 'five skinjobs walking the streets'. Since Baty, Leon, Zhora and Pris only add up to four (and a subsequent scene confirms Bryant wasn't counting Rachel in his first statement), the fan theory that followed was Deckard was the fifth one. Obviously, this has since been rendered null and void as the more recent cuts of the film redub the line to 'four skinjobs'.
Answer: Rachel asks Decker at one point if he had ever taken the replicant test himself, and he doesn't answer. Even though the movie itself doesn't seem to stress the point, in the book on which the movie is based "Do androids Dream of Electric Sheep?", the question of whether the protagonist detective is an android is the main theme.

Question: *Spoiler* What is the weapon that Sentinel Prime uses to kill Ironhide? It seems that all of the other Transformer weapons fire explosives or bullets, but his seemed to disintegrate Ironhide after he shot him.
Answer: the weapon is called an "Acid Rust Blaster" which seems to be similar to the cosmic rust seen in the animated series. the rust eats away at the Transformer's metal body.

Question: How did Carolyn get out of the cave and make it to the ship without being killed?
Answer: She had a jar of the light bugs that kept the creatures away.

Question: Why were the enforcers called sandmen?
Answer: In popular American lore, the Sandman is responsible for putting sand over your eyes to make you go to sleep. In this context the "sleep" is a euphemism for death, and the enforcers are responsible for making sure that everyone dies on time.

Question: O says that back in Cape Canaveral, in the unaltered time line, something happened to K that changed him. All that's really said though, is that he stopped and arrested Boris the Animal there. So what exactly was it that changed K?

Question: In the openings scene, the prehuman drinks a tar-like fluid (like the one poisoning Halloway later on), while looking at a spaceship hovering above. He then dies, falls into the river and disintegrates. I do not understand this scene, is he the last of the surviving prehumans committing suicide and the ship above is the others leaving the planet?
Answer: The giant ship has landed on Earth to drop off the Engineer so that he can terraform the planet and make it sustainable for life. He might drinks the black stuff to break down his own structure and spread life on Earth through his own DNA.

Question: What did Lisa turn Chet into? Every time I've seen this movie, I could never figure it out.

Question: Victor got his powers when his suit fused with him. Ben got his when he got pelted with rocks. Johnny was blasted with fire which explains his ability. But, how did Sue and Reed get their abilities?
Answer: It is believed that the heat from the radiation caused Reed to start "melting", which is how he got his rubber powers. It is unknown why Sue got invisibility.

Question: Why was Beethoven arrested? He wasn't doing anything illegal.
Answer: While it's not unusual for musicians to try out new instruments (playing a few rifts and even entire compositions) in a music shop, Beethoven's extended sampling-keyboard performance went wild, drawing an enthusiastic mall crowd into the relatively small music shop. The shop manager no doubt felt overwhelmed and called in mall security to clear out the shop before any damage and/or theft occurred. Keep in mind that the security team was already scrambling to respond to several simultaneous disturbances throughout the mall, all caused by 7 strangely-dressed oddballs (more than half of whom only spoke obsolete dialects and ancient languages). The time-travelers were, thus, probably all perceived as one group of pranksters or escapees from a mental institution.

Question: How exactly does the Merovingian protect the obsolete programs such as the twins from deletion?
Chosen answer: Obsolete programs are given the choice of deletion or exile. The Merovingian takes them in and, with his abilities to code the Matrix, allows them to stay under his protection.

Question: How did Snake lose his eye?
Chosen answer: During a mission known as the "Leningrad Ruse." He and his flight squadron were sent unknowingly on a suicide mission. During it, his goggles cracked and let in a poisonous gas, paralyzing his iris. He has to wear the patch because his eye can't focus against bright light, causing pain. This is mentioned in the novelization.

Question: I don't quite understand why Dr. Manhattan had to kill Rorschach. That is, I don't quite get why that was the only solution. Rorschach was a valuable member of the Watchmen, and in the type of world they were in (chaos, corruption, murder, etc) one would think that they would want to keep as many of themselves banded together as possible. Couldn't some sort of negotiation or compromise have been reached/agreed to by Rorschach instead of him being killed?
Answer: He has spent years as a costumed vigilante despite the fact that it was illegal. He has a very strict idea of what is right ("never compromise") and has proven himself incapable of doing otherwise. So no, there was no real chance of negotiating with him - Rorschach himself made it clear he'd have to die if they wanted his silence.
Death was not the only choice. Doc M could easily have teleported/banished Rorschach to Mars/anywhere secluded in an oxygen bubble. He could have spared his life and just made him mute or manipulate his brain chemistry/atoms to remove the memory of what happened. The point is Doc M is all powerful and could manipulate matter at his whim; death was just a plot device creating a chance of an emotive martyrdom/sacrificial ending.
Ethically speaking, exiling him to Mars or erasing his memory of the event can be considered just as cruel as killing him, because then his agency is being taken away from him. Rorshach's malcontent with the situation poses a problem for the other heroes, and since Dr. Manhattan isn't willing to let him tell the truth of what happened, he obliges Rorschach's demand that he kill him instead.
Chosen answer: When Ra saw the bomb, he realised that it was a few seconds away from detonation. There wouldn't have been enough time to send it back.