This movie's poor box-office returns created a big one involving Dr. Samuel Sterns and his Start of Darkness. Though the studio was able to continue Bruce Banner's character arc with his appearance in The Avengers, the lack of direct sequels to The Incredible Hulk meant that we never got to see the fallout from Sterns using Banner's gamma-irradiated blood to turn himself into the Leader. This plot thread was eventually continued in the Fury's Big Week comic that was released as a prequel to The Avengers. In it, Sterns uses his new abilities to attack Black Widow, only to end up knocked out and taken into custody by S.H.I.E.L.D.. Additionally, Samuel Sterns is set to return in Captain America: Brave New World with Tim Blake Nelson reprising the role.
The even bigger plot thread was the final scene that showed Thunderbolt Ross partnering with Tony Stark to take down the Hulk. This was never mentioned in any of the subsequent films. This was explained in the short film The Consultant; S.H.I.E.L.D. sent Tony as a patsy to ruin the relationship with Ross after the World Security Council ordered Fury to add the Abomination to the roster of the Avengers.
The New Avengers at the end of Avengers: Age of Ultron were hyped up as a replacement roster because of Tony retiring, Hulk going missing and Thor leaving to look for the Infinity Stones. They proceeded to do one onscreen mission in Civil Warnote during which War Machine and Vision, two of the new members, are completly absent which lead to the eponymous conflict and then quietly disappeared until Avengers: Infinity War 3 years later, in which the Downer Ending has most of them being snapped away and leading to the original Avengers coming back together for Avengers: Endgame.
Thor's Achilles in His Tent storyline does get a resolution when he comes back claiming to have had "a vision" but what was meant to be a longer storyline ended up mainly a Missing Trailer Scene.
Thor's vision of Asgard was supposed to setup Thor: Ragnarok. Depictions of the Asgardians descending into decadence, demonic musicians, and Heimdall being blinded were all meant to foreshadow the events of the upcoming film. Once Taika Waititi was brought on board as the film's director, Ragnarok underwent a complete Tone Shift and much of the imagery seen in Thor's vision went unused.
Shortly after Ghost reveals Hank Pym's role in her father's death, Hank defends himself by claiming that Elihas was a traitor who deserved to be fired, for reasons he doesn't elaborate on (apart from being a Mythology Gag to Elihas being Egghead, one of Hank's major supervillains in the comics). There is no followup or clarification on this later on — it never gets brought up again.
Hydra agent Mitchell Carson got Pym particles in Ant-Man. If he ever used them, it has never been addressed. That being said though, there was originally going to be a post-credits scene for the movie where Mitchell got his just desserts as Scott Lang stealthy ambushes Mitchell's office to get the stolen particles back. Whether or not if it's canon, we will never know.
Doctor Strange (2016) ends with Karl Mordo being disillusioned with the Ancient One and leaving on a mission to purge the world of magic users; heavily implying that this was going to the main conflict for the sequel. However, outside of a brief mention, there is no appearance of the original Mordo at all in Doctor Strange in the Multiverse of Madness and instead we encounter a variant of him from another universe. There is also no mention of his on-going mission to rid the world of magic users and an art concept book implies that he was possibly killed by the Scarlet Witch.
Spider-Man: Homecoming ended with Adrian Toomes aka The Vulture aware that Peter Parker is Spider-Man but refusing to disclose his identity out of gratitude for Peter saving the lives of him and his daughter. In The Stinger one of Vulture's accomplices, Mac Gargan makes it clear he doesn't buy Vulture's claims of not knowing Spider-Man's identity and will pry the information out of him to get vengeance. Neither of the film's sequels features Toomes or Gargan (meaning Gargan has yet to take on his costumed identity of the Scorpion, which some fans thought Homecoming's ending was setting up), and the end of Spider-Man: No Way Home has all memories of Peter Parker being erased from the universe, making it impossible for the plot thread to resume. However, it becomes subverted when he turned out to have been teleported into Sony's Spider-Man Universe by the same spell that erased Spider-Man's identity, as shown in Morbius (2022), and seeks to form the Sinister Six with him.
At the close of Avengers: Endgame, Thor, seeking a fresh start, leaves Earth behind and joins up with the Guardians of the Galaxy. This status quo is quickly abandoned in Thor: Love and Thunder, which sees Thor part ways with the Guardians (who have already grown tired of him) and return to Earth within the first act. Guardians of the Galaxy Vol. 3 was planned to not feature Thor whatsoever regardless of what Love and Thunder planned to do with him as a Guardian, so in the long run, it at least provided an explanation for his absence.
Black Panther: Wakanda Forever has Everett Ross on the run from the CIA after he's caught illegally helping the Wakandans. Come Secret Invasion (2023), he's working with Nick Fury, a member of the American government, as well as other CIA agents, without explanation.
Live-Action TV
Iron Fist: At the end of season 1, Madame Gao is seen in Paris as she overhears Joy and Davos plotting to kill Danny. Since Gao dies in The Defenders (2017), her potential involvement in season 2 is cut short.
Jessica Jones: At the end of season 1, Will Simpson remains at large, still pining for Trish and hopped up on super-soldier serum. He's reintroduced in season 2 following Trish in a few early episodes, then gets suddenly killed off-screen by Alisa, ending that plot line rather abruptly.
Luke Cage: In response to Cottonmouth declaring that it's impossible to kill Luke due to his bulletproof skin, Mariah ominously suggests that bulletproof skin wouldn't stop him being drowned or poisoned. No-one ever ends up actually trying either of these options.
An in-universe example. Much of the conflict in the early episodes is derived from Wanda and Vision having to hide their superpowers from the residents of Westview. However, as the series goes on, both characters use their powers in full view of these people, who don't seem to have any reaction. This is showing that the Show Within a Show is "losing the plot" while the reality of the situation becomes harder and harder to ignore.
The Stinger ending of the show has Wanda using the Darkhold when she hears her children crying out for help. Doctor Strange in the Multiverse of Madness ignores this and instead has Wanda trying to gain the power to travel to another universe where her kids are alive, well, and not in any kind of distress that would lead to them calling her for help.
