Spoilers ahead, so do not read if you're not up to date with Marvel Movies.  and maybe this is a silly or unanswerable question but it bugged me after watching Spiderman homecoming.  During Civil War, I don't remember the exact quote but Tony said she'd left him and it sounded pretty final.  At the end of Spiderman Homecoming there was talk about a marriage proposal (somewhat jokingly as the real announcement didn't happen).   The obvious answer I suppose is that they got back together, though that as never explained and, frankly, seems like bad writing.   It was nice to see her make a cameo, but is there any official word on this?   Did they split and get back together?  Part of me thinks this is a really dumb question where that's the obvious answer, but I'm still a little bit curious if there's more info on this anywhere.
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I really don't know how to do this in terms of spoilers, but here goes...  After watching the end of Homecoming, it appears that       Tony and Pepper are very much back together.   Is there any in-universe explanation for this change from the way the universe seemed to be in Civil War?
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In the "End Credit" scene of , we saw Maria Hill and Nick Fury driving in the street and then there was a message on the radio. Nick then asked Maria, "what is it?" Maria answers, "Multiple bogeys over Wakanda, more powerful than New York". After that, they turn into dust by the snap. So that means when they were talking, at the same time Thanos was trying to snatch the Mind Stone, or already did, and was ready to snap.   Now the main point; all those "space-crafts" carrying Thanos' armies landed over Wakanda much earlier. Then what were those "multiple bogeys" Maria referred to? What was going on over there at that moment?
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At the end of First Class, Xavier is paralysed, and him and Magneto split paths. However at the beginning of Last Stand, it flashes back 20 years, and you see the grown up Xavier and Magneto, friends, talking to a young Jean Gray.  Did Xavier get the use of his legs back and then lose it again?  Or is this just a continuity error?
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So, Michonne's pet walkers: who were they, and where did they come from? Is it ever revealed?  I guess this question would be directed more towards the comic book fans, since the best answer in the show has been "they deserved what they got, they weren't human to begin with". Other that that she always clams up at the subject.  I have my theories, but because she is so reluctant to reveal anything about herself it's really difficult to put any stock in those theories...
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In the film Captain America: The Winter Soldier, a flashback explains how     Bucky was 'recovered' after his fall from the train.   I can't recall whether it is explicitly stated that he fell into the custody of the Soviet Union, but I know this to be the case in the 616 and he speaks Russian in the film.  The bunker under Camp Lehigh contains      Arnim Zola, who provides a piece of expository dialogue describing how he was acquired through "Operation Paperclip", colloquially known in Europe as The Brain Drain.   At the conclusion of WWII, Europe was divided up between what would eventually become the EU and the USSR. In order to keep players off the table, a great number of European 'assets' were repatriated as Americans:     Arnim Zola being one of them, and it is implied that the Winter Soldier is another.   If the Winter Soldier was already a Soviet asset, how have HYDRA (a German/American brain-drain coalition of Fascism) come to be in possession of him? If the Soviets created the Winter Soldier as a weapon against American-Intelligence/HYDRA/SHIELD, why is he fighting on their side? does the film explain this at all, or have I missed something?
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Did Frodo take it off? Or was the fell spider's sting simply too strong to be stopped by Mithril?  If it is the latter, that would be pretty surprising, because that would mean Shelob could possibly sting a sleeping dragon! (I remember Gimli saying "Mithril... hard as dragon scales!")
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There is this one little thing that I don't quite get at the end of Avengers: Endgame.  After Thanos was defeated, Captain took the stones back to where they were originally taken to "correct" the timeline. However we see that Cap has the 6 stones in their "Raw" form, but that is not how all of them were taken.   For example in 1970 Tony didn't take the Space Stone but the Tesseract, so I assume they extracted the Space Stone in the present (by breaking the Tesseract like Thanos in the Infinity War movie?).   So how could Cap return the stone to the rightful place when he actually needed to return the Tesseract? Or am I missing something here...   The same goes for the Mind Stone, which was inside the Gem on the Staff Loki had in the first Avengers movie.
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If Steve Rogers, as Avengers: Endgame has shown, never went on the ice to go to the future to form the Avengers, then the current timeline doesn't make sense. Also if he went back before he went on the ice, then what happened to the other Captain America in general?  If he went back after the past Cap went on ice then that would mean that there are now inconsistencies with Winter Soldier and Civil War where Peggy is mentioned as to have already lived a life without him.
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Near the end of Captain America: Civil War we learn that      Howard and Maria Stark were assassinated by the Winter Soldier   and Captain America admits that he already knew.  But how did he find out? I don't recall this being revealed in any of the previous movies, and I can't think of a reason why the characters who already knew would have gone out of their way to tell Steve about it.
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Why can't the Avengers in Endgame go back in time to 2016 and bring Black Widow from 2016?  They can explain her about Infinity War and Endgame. I'm sure she can understand, considering the fact she knows everyone has superpowers and the explanation sounds reasonable.  This is similar to how Star-Lord is trying to find Gamora.
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I noticed in Spider-Man's recent cameo in Captain Marvel, he appeared an awful lot like Andrew Garfield who is playing Spider-Man in the recent movie.    Irrelevant of whether it is just my imagination, do some depictions of comic characters morph to be more like an actor who plays them around the time a corresponding movie is released?  By comparison, here is Spider-Man's depiction in the Spider-Men crossover:
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Towards the end of Avengers: Age of Ultron JARVIS uploads himself into a lifeless Virbranium android. This process creates Vision. Then before the final battle we see Tony Stark uploading a program called FRIDAY into his suit. During the battle we hear a feminine voice in The Iron Man suit instead of JARVIS'. So did JARVIS cease to exist after uploading himself into Vision? If so did JARVIS know that this would happen, or was it because of the Mindstone?
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I am not a physicist, however, when Barry is running/flashing, he gets to talk to the team back in HQ - How?  When he talks back to them, I have a feeling, his voice needs to be distorted, even if not possible, as everything is ultra fast with him.  Isn't there some law in physics, that the movie is breaking, by allowing him to talk normally (vocal cords, breathing) while moving at 1000's steps per seconds (or whatever?)
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So there are two teams in Avengers: Endgame: Natasha (Black Widow) and Clint (Hawkeye)/Nebula and War Machine.   Yet Black Widow and Hawkeye were chosen for the mission to Vormir. So did Nebula know to send them since one loved one had to be sacrificed and she gathered that they both share a history or was it just a normal team separation?
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In Avengers: Endgame, Thor brings back Mjolnir (his hammer) from the past to his "future" self through the quantum tunnel. Later in the movie, Captain America gets hold of it being worthy.  However, I don't remember if Cap takes it back to the past in the climax. If he doesn't - that would break the spacetime continuum, Mjolnir being destroyed in the past.  If he does bring it back, how come he knows the exact time and place to return?
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Sorry, not quite sure how to format spoilers so I tried to keep the title vague.  Here's for the new Thor movie (just watched it last night):      How did Loki fake dying (and managed to fool Thor, the reinforcements who found his body and possibly Odin since he would have wanted to see the body after it was brought back)?   And follow-up:      Also, in the end, he's shown to have pretended to be Odin on the throne while talking to Thor about Thor's decision to stay on Earth. Where is Odin and how did Loki manage to do this? Did he do something to Odin?
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In Age Of Ultron we witnessed Hulk lose a tooth.   My question is: Has Bruce Banner lost a tooth as well?