These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Dan Slott (who has a flair for these) supplies a humorous one in the final issue of Vs. for a couple of the more ridiculous victories in prior issues. Turns out Squirrel Girl and Pixie, completely ignorant of the conflict, were playing an RPG with the Puppet Master's voodoo dolls. It's somewhat unclear whether this was intended to be canon, but more than a few fans accept it.
Broken Base: This event should have been titled "Avengers Fans vs. X-Men Fans".
Either you think the Avengers were assholes who came to San Francisco in bad faith ready to kidnap a kid for dubious reasons with no intentions of negotiating or you think that they were justified because the Phoenix is a giant threat and they have to do anything necessary to stop it from potentially destroying everything.
Either you think that the portrayal of the Phoenix as a destructive entity is fine and in line with the most well known Phoenix story (the Dark Phoenix Saga) or you feel like it's a flimsy premise that ignores 15-20 years of Rachel Summers' existence and her bonding with and complete control of the Phoenix Force.
Either you think that the actions of the Phoenix Five are in line with the corrupting influence of Phoenix Force or that things are being wildly exaggerated for dramatic effect with the main group being written incredibly out of character.
Either you take it as given that the Phoenix Five made the world a utopia, or you take it as a given that they did so by quashing free will across the planet.
Either you think this story is the natural climax/ending of Cyclops' character arc since Messiah Complex or you feel that his Jerkass qualities have been taken over the top to justify the actions of the Avengers.
If not, you either consider Cyclops a villain who's finally getting what he deserves, or you think he's basically a victim to the Avengers who's been pushed to the very end.
Either you think that Captain America was right in presume over Scott's mental condition, and his lack of open remorse is evident of his fall from grace, or you think he's a detached political sock puppet incapable of recognizing how Scott had been carrying on his shoulders a situation for years so impossible that if one, and only one of his friends dies in an attempt to stave off genocide, (of the usually hate induced variety), rather than say, a bus full of children, then it was in fact a very good day,and think Cap's reaction to his imprisonment are, at best, embarrassing.
Everything in the story and even the very existence of the story itself really is grounds for heated arguments. Which is probably the point, really, as the Avengers and X-Men have wildly different ideologies and themes that are often debated even when the characters themselves aren't punching each other.
Conflict Ball: This ball gets volleyed back and forth so much throughout the event that this might as well have been the Olympics. Specific examples aside, many of the people involved have worked with each other and are friends, and much of the event could have been averted if some of them sat down and talked like adults.
The Avengers and anyone siding with them. To X-Men fans, they've spent the entire story acting like giant antagonistic jackasses and are essentially responsible for most of the bad things that happen (Mainly by showing up, telling Cyclops they're taking the potential savior of his near extinct race and that's that; and again when Iron Man's "brilliant plan" causes the Phoenix Force to be split and create the Phoenix Five). Issue 11 pretty much pushes it over the top despite the fact the Avengers are, nominally, the heroes of the story. Acknowledged in the last issue, where Captain America realizes that the Avengers have been pretty crappy heroes when it comes to mutant affairs.
Wolverine specifically fell under this early on in the story, as his solution to dealing with the Phoenix was to outright kill the teenage girl who was the intended host before the Phoenix arrived, which went much farther than the Avengers merely wanting to take Hope off-world in the event that she was unable to control the Phoenix. However, he soon backed down from this line of thinking when he realised he couldn't go through with killing a child.
Designated Villain: Cyclops' X-Men, and later the Phoenix Five. At least, until they become corrupted by the Phoenix Force & start acting more like actual villains. Even then, Cyclops could still be a designated villain, as he only gets consumed by the Dark Phoenix after much poking and prodding by the Avengers and the X-Men. Until that point he had kept his sanity, at least compared to his teammates.
Magnificent Bastard: Cyclops is an Anti Heroic example, particularly in Consequences where he displays that he knows how to play him some serious politics.
Moral Dissonance: In he end, the Phoenix Five are punished, with Cyclops being regarded as a war criminal. Never mind the fact that they were mind controlled by the Phoenix and shouldn't be held responsible, but many of the people condemning them for their actions have also committed crimes while not themselves, but also Cap's behavior during the whole debacle is very similar to the way Tony Stark acted during Civil War, which Cap was violently against. Add in the fact that the whole mess and every time it escalated was directly the Avengers fault, making Cap, the Avengers, and the X-Men that sided with the Avengers come off as very hypocritical.
Emma has two possible moments thus far. In the Avengers Academy tie-in, she scraps Juston Seyfert's pet Sentinel, simply for being a Sentinel, while in issue 9 of the main series, she telepathically kills a man who had killed a mutant child thirty years ago in a hit and run, and kept it a secret.
Namor's assault on Wakanda, which likely killed countless civilians.
The prison where Scott is being held in Consequences crosses when they allow Scott's new friend, a newly-activated mutant, to be lynched by the other inmates. This causes Scott to accept Magneto's offer to break him out.
Narm: In issue 11, Iceman tells Xavier that he considers Scott his brother, but he can't let him carry on down the path he's headed anymore. Fair enough, but why is it narm? Havok, the actual younger brother of Cyclops, is in the background as Iceman says this.
After an entire summer event concerning superhero on superhero violence, we finally get a scene of Captain America humbly coming to a power he cannot control, admits they have been unfairly estranged for many years, and begs it for help against the coming threat. By which he means The Hulk, rather than the godlike being whose granddaughter he kidnapped. It's hard for a reader to forget that had he done that in issue 1, the whole thing would have been avoided.
They Wasted a Perfectly Good Plot: Interested in seeing what this utopia the Phoenix Five created is like? Too bad! The reader is merely told that they P5 made the world a perfect place. Actually seeing any of that, examining the morality of a benign dictatorship, seeing what the ordinary person thinks about the benevolent cosmic-powered mutants who took over the world, etc., would get in the way of more punching.
Black Panther annuls his marriage after a fight with his wife. The same fight where Storm declares that she no longer wants to be married to Panther and throws down her wedding ring. Also worth noting is that Panther was on the defensive the entire time during the fight.
If the Phoenix Five takeover made the Earth a utopia, the story might seem to argue for some form of benevolent dictatorship, which is rather at odds with years of stories about the likes of Doctor Doom and Korvac.
Averted with regards to questions about just how the P5 successfully resolved certain extremely contentious real-world conflicts that have been shown to exist in the Marvel Universe, because most of this happens quietly off-panel during the time skip.