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.
When Leinil Yu was providing artwork for the series, he continued to include Iron Fist in his classic costume even though the character had debuted a brand new costume a few months earlier in The Immortal Iron Fist, and constantly featured Howard the Duck in group shots of various heroes not in the team.
BLAM Episode: The storyline about Nick Fury and the '50s Avengers, which has no bearing on the series, and aside from one miniseries has never been mentioned again.
Creator's Pet: Luke Cage for Brian Michael Bendis, whose run on the book saw him go from Hero For Hire to leader of the New Avengers, and is one of three characters (The others beingWolverine and Spider-Man) to remain on the team for the entirety of the first two volumes. While he did become a more mainstream character under Bendis, many grew tired of his exposure over the years.
Similarly, Jessica Jones, who was merely a supporting character in the first volume before becoming a full fledged member of the team following Dark Reign and actually was created by Bendis. While she was initially a very liked character, especially due to Alias, fans grew tired of her very quickly, due to her seemingly needing to be in everything.
Hilarious in Hindsight: In an early issue of the series, Daisy Johnson is needed and afterwards, she declares that her Avengers codename will be Quake. Steve then informs her that they aren't looking for new recruits. Years later, during Hickman's Avengers, Tony and Steve are expanding the lineup, and right there on a list of recruits is Daisy Johnson.
Ho Yay: When the embarrassing truth came out that Jessica Jones had a crush on Peter Parker when they were in high school came out, Spider-Man attempted to reassure Luke Cage that he had no designs on his wife. He then went on to ask if the way were clear to Iron Fist...
Mary Sue: Fongji, a previous Iron Fist who manages to acquire the power of the Phoenix as well, before vanishing for parts unknown. It doesn't help that she looks incredibly like Hope Summers, who's received similar accusations.
Narm: Ms. Marvel's idea of an insult? Calling someone a "hump".
The Scrappy: The Sentry is universally hated by this point.
Tearjerker: Luke Cage's attempts to find and reconnect with his father, who is unable and unwilling to look at his son, much less talk to him.
They Changed It, Now It Sucks: The reaction a number of "old school" Avengers fans had, with the initial line-up featuring only two classic Avengers and the shift away from the global level threats the classic book dealt with.
They Wasted a Perfectly Good Plot: In the opening story of vol 2, it's stated that the Vishanti, the Big Good as far as magic is concerned in Marvel, are no more. Despite the fact that this should be a world-shaking event, it's never brought up again.
Audience-Alienating Premise: A lot of people are pretty quick to turn away from the book, mostly because of the reputation of being about how morally reprehensible the main characters can be.
It doesn't help that there are other groups that are actually being more productive with coming up with a solution to the problem that doesn't involve blowing up other Earths. When Doctor Doom is doing a better job of doing that, well, so much for the smartest 'heroes' on the planet...
Evil Is Sexy: Black Swan seems to have developed this reputation.
Ho Yay: Sun God doesn't go berserk as his team is destroyed, but when the Rider, Wayne, dies. It helps that the two are very clearly Expies of Superman and Batman, respectively, who are the poster boys for the trope in comics.
Strange either already crossed it when he offered to sell his entire soul for power before finding out that it was already bound to another demon or at the latest when he slaughtered the Great Society with those dark powers.
While one could make an argument in favor of Namor for saving Earth 616 via destroying the homeworld of the Great Society, he most definitely crossed it after gloating right in T'Challa's face how he enjoyed destroying Wakanda twice and regrets that so many are left alive. Although he was mourning the death of his own people the second time, which Shuri is directly responsible for, so he may not have meant it.
Nightmare Fuel: The reveal in "Time Runs Out" that without any warning whatsoever, almost every single universe in existence has just... vanished.
Villain Sue: The Ivory Kings. While being able to defeat the Celestials is plausible, being able to kill Infinity and Eternity, not to mention the Living Tribunal, the second most powerful being in all of Marvel's cosmology, most certainly isn't.