Blooper: The second season contains plenty. For example, in "Who Do You Trust?", Tony's jacket disappears in between shots, and the closing scene of "Secret Invasion" shows Nick Fury wearing his eyepatch on the wrong eye.
Vision gets badly damaged at the end of "Ultron Unlimited," yet "Yellowjacket" shows him alive and well, but the viewers' assumptions that he got fixed in between episodes become dashed after "Emperor Stark" begins with him getting repaired. You can't assume that "Emperor Stark" takes place before "Yellowjacket," either, since JARVIS shows Yellowjacket helping take over Europe.
Executive Meddling: The last episodes of the first season aired in other countries well over a month before they will air in the US, because Disney/Marvel wanted to finish out the season to match up with the releases of the Thor and Captain America movies.
The second season deviates from overarching stories and ends with 12 self-contained episodes, because the children in the test audiences had less trouble following one-part stories. Also, those episodes place an increased focus on Iron Man, Captain America, and Thor, for the convenience of viewers more familiar with the Avengers from the Marvel Cinematic Universe than those from this cartoon, or those from the comics. This is literally a case of executive meddling, since it was at the directive of the new producer Jeph Loeb.
Even worse, we were left with many unresolved plot lines. We never saw a Civil War style story (which is arguably for the better or for the worse) and Surtur became a Karma Houdini, as his story was not finished.
Ultimate Spider-Man has become a cause of great misery for EMH fans, and not just because the next Avengers cartoon will apparently share its universe. Producer Josh Fine's Twitter page says that Marvel Animation managed to reach episode 39 by June 2011, but a later panel at Comic-Con revealed that Disney XD will not air episodes 27-52 until the release of Ultimate Spider-Man...in 2012. Then, after Ultimate Spidey earned an undeniably large hatedom, Disney XD decided to run some new Ultimate Spidey episodes without new Earth's Mightiest Heroes adventures after them, to see if the Avengers deserve the credit for Marvel Universe's ratings. Then, three Earth's Mightiest Heroes episodes guest-starring JoshKeaton as Spider-Man got redubbed by Ultimate Spidey's VA, Drake Bell, apparently without Josh's consent or even knowledge. A Twitter movement for getting Marvel to release the undubbed versions has begun, though it failed to get Disney XD to air those versions.
On the bright side, only two or three Ultimate Spider-Man episodes aired without a new installment of Earth's Mightiest Heroes afterward, and some weeks also saw fans of neither show get anything new.
Lying Creators: In the season 2 promo included on Disney's first DVD, Chris Yost and Josh Fine show some model sheets for the Captain America Skrull, and comment them in a manner that makes it sound like the real Avenger undergoes a costume change.
At least one other interview promised that Jeph Loeb's retool would dedicate more screentime to Iron Man, Captain America, Thor, and Hulk, who had each started in at least one live-action movie prior to the second season premiere. Of the 12 episodes Loeb executive-produced, Hulk only appears in two.
No Export for You: DVDs in the United Kingdom lack the episode introducing Captain America, Bucky, Wolverine, Red Skull, and Kang the Conqueror.
Recycled Script: "Powerless!" has some plot elements copied from Thor's movie. Namely, Thor becomes a mortal, Loki tries to kill him with Destroyer armor, Thor sacrifices himself to protect mortal companions from the Destroyer, and Thor regains his hammer and his immortality as rewards for his selflessness.
Screwed by the Network: This show got slightly "screwed by the cable companies", as Disney XD was dropped from most basic cable packages in the US right around the time the show premiered, leading to a lot of frustration from fans who want it to be put somewhere more easily visible.
Marvel's video website used to have the complete first season available for free streaming, but it later disappeared without warning or explanation.
Marvel stopped regularly posting episode previews in between the slowing down of The Avengers' box office performance, and the buildup to the movie's home video release.
Speaking of The Avengers' box office performance, what did Disney XD do with this show as the movie made the top 10 of every weekend during the month of June? Show no new episodes at all.
Graviton and Hulk have the same voice actor. This goes on into Season 2, where Fred Tatiascore voices Hulk and the Thing, who spend most of their episode arguing and fighting. Red Hulk also has this same actor.
Rick D Wasserman also voices Thor and the Absorbing Man, who have a fight in "Gamma World" while exchanging battle cries.
Baron Zemo and Abomination are both voiced by Robin Atkin Downes, and the it turns out that they are the two Masters of Evil who argue the most.
Vanessa Marshall does this when Black Widow shows Madame Viper the vial of Hulk blood she stole.
Josh Fine in an interview says if he continued to helm the series for a third season, said season would have been the "Magic Season" (Season 1 being the Assemble Season, Season 2 being the Cosmic Season). He didn't go into too much detail, but some have speculating that Doctor Strange, Dormammu, the Scarlet Witch, and other characters would have shown up. He's also mentioned that Tony and Maria's conversation about registering super-heroes from episode 28 would have been followed up. Apparently, Fine even had some ideas for a FOURTH Season, but hasn't given any details.
The show contains elements from what was originally going to be a Hulk series. This is probably why many of the Hulk's Rogues Gallery appear on the show since they don't normally menace the Avengers (aside from Absorbing Man).
Some of the first choices for the Avengers' foe in "Breakout, Part 2" included Doctor Doom and Magneto. However, it apparently seemed inappropriate for "Earth's mightiest heroes" to team up and defeat someone another superhero team had fought many times before.
This trailer boasts voices and animation that differ from the actual show.
The lyrics to an extended version of "Fight as One" would have included these.
Mockingbird was due to join the Avengers, but it became too expensive to have EG Daily voice a major protagonist.
In an interview with Josh Fine, he said that they would have liked to introduce Taskmaster in Season 3.
Chris Yost wrote on Facebook that "Emperor Stark" started out as a faithful adaptation of a graphic novel titled, Emperor Doom. This would have necessitated bringing Simon Williams, the hero of that story, Back from the Dead.
The original writers wanted to put Earth's Mightiest Heroes in the same continuity as Wolverine and the X-Men. Chris Yost once wrote in one of Marvel's live blogs that they take place in the same universe, but later said that the swift cancellation of Wolverine and the X-Men ultimately put a damper on these hopes.
Captain America was originally supposed to fight the Nazis in the World War 2 flashbacks, but Executive Meddling meant that the creators could have either realistic firearms or Nazis, but not both. They went with the firearms.
The solicit synopsis for the twelfth issue of the Marvel Universe comic series suggests the existence of an unreleased comic placing the Avengers and Loki in an Enemy Mine situation.