When Stan Lee created Marvel's heroes, he was living in New York, so he placed his characters in the place he knew and loved. The X-Men lived in Westchester, Spider-Man was based in Queens, and Avengers Mansion was right in the heart of Manhattan.
But the problem with having them in such a populated area is that superheroes tend to cause a lot of destruction when they get into fights. Cars and buildings regularly get demolished, and considering how squishy most humans are compared to the average skyscraper, it should be no surprise that civilian casualties can be truly horrific. Such deaths are tragic, but even more horrific is the fact that the Avengers have been responsible for the destruction of New York...and that this has happened on multiple occasions.
10 Asgardian Avengers Enabled The War Of The Realms
The War of the Realms was one of the most devastating events in the history of the gods. The dark elf Malekith the Accursed invaded each of the Ten Realms, one by one, conquering them for himself. Finally, he invaded the Earth, destroying New York in the process. The whole city had to be evacuated by Stephen Strange as frost giants ripped through it.
However, this was preventable. Marvel's Thor and Odin both had chances to stop Malekith but didn't. Thor is a founding Avenger, while Odin was one of the Avengers of 1,000,000 BC. In fact, much of the story building up to the War involved Odin fighting with other Marvel characters and preventing them from doing what they needed to stop Malekith. Such infighting allowed Malekith to build his armies.
9 The Young Avengers Let Iron Lad Cause A Time Paradox
The Young Avengers may not be the main Avengers team, but most of them have been embraced by their adult counterparts. One of them who has not received this blessing is Iron Lad, who is actually a time-displaced younger version of Kang the Conqueror.
Iron Lad did not want to grow up to become a despot, so chose to go back in time and become a superhero. However, this created a time paradox and ripped New York (and much of the world) asunder. The damage was only repaired when he was forced to return to his own time.
8 Avengers Disassembled Also Caused New York To Disassemble
When Scarlet Witch had a psychotic break, she accidentally used her powers to take down the entire Avengers team...and much of the city around them. A dead hero returned to life, then exploded in the Avengers mansion. She-Hulk involuntarily Hulked out in downtown Manhattan. And amid the many, many other horrible things to go wrong, a Kree invasion fleet appeared in the sky, raining down death from above.
The city mostly recovered when Scarlet Witch's magic was counteracted by Doctor Strange, but lives were still lost and much of Manhattan was horribly damaged. On top of that, the Avengers disbanded, brought down by one of their own members.
7 The City Was Plunged Into Darkness In Secret Empire
Red Skull used a sentient cosmic cube to alter the past and retroactively make it so Captain America had always secretly been an undercover Nazi. Because that's the sort of thing that happens in comics. This led to Captain America working with Hydra, then taking over the entire Earth in the Secret Empire story.
One way that he maintained a stranglehold of control was that he had New York plunged into perpetual darkness within the Darkforce Dimension. Many of Earth's heroes were in New York at the time. The city was eventually rescued (and the cosmic cube's damage reversed), but it is tragic to think that Captain America would do that to the American city he grew up in.
6 Fear Itself Resulted In The City Being Torn To Shreds
At the start of Fear Itself, Red Skull's daughter Sin took control of a secret Nazi base in Antarctica, unleashing magical hammers and Nazi mechs upon the world. These mechs destroyed major US cities, including New York, reducing them to rubble. On top of that, the Thing was possessed by one of the magic hammers. He turned evil and smashed downtown Manhattan.
It is easy to say that the Thing is the only Avenger who destroyed any of New York. However, if there has been a Nazi weapons facility sitting around for decades with a stockpile of mechs and death magic, it seems like Tony Stark and Steve Rogers bear some responsibility for not handling this threat sooner. Their job is to protect the Earth, and Stark's satellites would have seen the huge fortified concrete installation surrounded by Nazi bulwarks sitting in the middle of the Antarctic ice sheets since the 1940s.
5 Wolverine Created A Dystopian Alternate Timeline In Age Of Ultron
Wolverine is a fearsome killer, a dedicated teacher, and an experienced field commander. He is not skilled at the complex intricacies of time travel.
Despite this, during the Age of Ultron story, Wolverine stole a time machine, went back into the past, killed Hank Pym before he invented Ultron, then returned to the present. He hoped to stop Ultron before the evil android was ever created. Unfortunately (and predictably), killing a founding Avenger like Pym had colossal ramifications for the timestream. Wolverine rewrote all of reality, including New York. The city became a dystopian nightmare. Just before he left to undo his mistake, a helicarrier crash-landed in the city, blowing it up.
4 Hank Pym Is Responsible For Ultron's Actions In Age Of Ultron
Hank Pym created Ultron, and so he bears some responsibility for Ultron's actions. After all, Ultron is an artificial intelligence, designed by Pym.
In the Age of Ultron comic, the evil android obliterated numerous cities with bombs and projectile blasts. Most impressive of all, he apparently phased an entire high-tech future citadel through the city of New York. He also remade a future version of the city in his own image. Pym may not have done this himself, but he shares responsibility.
3 MCU's Avengers Are Culpable For Everyone Thanos Killed With His Snap...Including The People Of New York
At the end of Avengers: Infinity War, Thanos brought his armies to Earth to retrieve the Mind Stone, which was located in Vision's head. The Avengers understood that once Thanos acquired the Mind Stone, he could unleash widespread devastation. Such devastation was preventable, but it would mean killing Vision. Captain America argued "we don't trade lives."
This is a genuinely noble sentiment. Unfortunately, in war, one has to deal with the world as it is, and that can mean sacrificing one's morality. Such sacrifice is a slippery slope. But even Vision advocated for his own death to stop Thanos. Had the Avengers been willing to kill Vision without delay, Thanos would not have been able to wipe out half of all life in the universe. Since New York is part of the universe, the Avengers traded half of the lives there--including Vision's life--to stick to an abstract principle.
2 Marvel's Civil War Turned The City Into A Fascistic Police State
Civil War is considered a classic story, but it is also divisive among fans. Many heroes act out of character. Two of the world's smartest men, Reid Richards and Tony Stark, act in vexing ways, implementing policies that align with the fourteen attributes commonly used to identify a fascist government.
At the start of the story, the US government passed a law that required all superhumans to formally register their identities. Half of the heroes worked to enforce this, led by Iron Man, and the other half rejected this tyrannical idea, rallying around Captain America. The fighting in this "war" mostly took place throughout New York and the actual damage was minimal. However, since New York was where most superheroes lived, Tony Stark essentially transformed the city into a police state. Few buildings or people were harmed, but the soul of New York was damaged beyond recognition.
1 Knull Possessed The Avengers And Used Them As His Weapons
In King in Black, Knull, the god and creator of the symbiotes, led an army of symbiotes to invade the Earth. It can be argued that Eddie Brock and the Venom symbiote (who had once been part of the Dark Avengers when bonded with Mac Gargan) provoked Knull's attack. However, that may be putting too much blame on the victims.
Knull used his symbiotes to take possession of Earth's superheroes...and much of the rest of the populace. Then, he turned these heroes against the people and places they had once defended, and nowhere was hit harder than New York City.