Otogi/Duke in Yu-Gi-Oh!: He came close to inheriting the Millennium Puzzle in the manga, when his father lost a game for it against Yugi's grandfather, leading them to believe it should have been Otogi's.
In Jubei-chan, Yagyu Jubei passed on his power in the form of a "Lovely Eyepatch", eventually going to a girl hundreds of years in the future because he believed his heir had died in Russia. Actually, she didn't. She was just frozen in an iceberg. By an amazing coincidence, she dethaws in the same time period Jiyu receives the Eyepatch and is furious she didn't get it.
Well, Ken sort of missed the call. He did answer it for Wonderswan game Tag Tamers (which, naturally, wasn't released outside of Japan) to team up with Ryo, and they defeated Millenniummon, who was responsible for the dark spore in his neck. When Ken got back, Osamu got pissed off at him for touching the Digivice, and you know the rest. In a sense, he picked up the call, then dropped it.
Hikari also missed the call at the start of Digimon Adventure due to being sick. Coincidentially, her partner was in the hands of a Big Bad by then, having been lost as an egg and taken in by Myotismon... which raises the question of what would've happened had Hikari not missed the call and gone to the Digital World anyway.
Four random kids in Digimon Frontier, Katsuharu, Teppei, Chiaki and Teruo, ironically, miss the call to go home from the Digital World and end up just wandering around doing all of nothing while the real adventure is taking place on the other side of the planet.
Also in Digimon Frontier, Kouichi missed the call... because he fell down the stairs and died. However, he made it into the Digital World anyway, initially corrupted, but became good later on.
In Digimon Tamers, Ai and Mako got Impmon and became Tamers a lot earlier than anyone else, but because they were three or four at the time they were too immature for their partner to handle. He left them, and they subsequently missed out on adventuring to the Digital World and fighting the Big Bad up until the last minute possible.
In the BW arc of Pokémon Special, the call wasn't missed; it broke. Bianca and Cheren were chosen to be Dex Holders (which is a pretty big deal in this series), but unfortunately their Pokedexes were dropped into a puddle and short-circuited. Meanwhile, Black (who was also chosen) kind of ran off with the last Dex without seeing what happened to the other two. At least Bianca and Cheren still got their starters...
Now, it's beginning to look like Bianca and Cheren were never meant for the (main) call in the first place. Bianca gave her Pokedex to White, while Cheren's was eventually completely destroyed by N's Pokemon.
In Brigadoon: Marin and Melan, while Marin has an important role to play it turns out she isn't the "Creis". She helps save the world anyway.
In Fresh Pretty Cure!, after Eas is killed for turning against Labyrinth, the Red Pickrun confronts her and reveals that she'd always meant to be the fourth Pretty Cure, but couldn't get near her because of her evil influence. With her Heel-Face Turn and death, it's able to fix this problem, resurrecting her and allowing her to become the fourth Pretty Cure, Cure Passion.
A minor one from Code Geass: right at the beginning of season 1, when the Britannian forces are purging the Shinjuku ghetto, we see everyone's favorite Ensemble Darkhorse Jeremiah Gottwald verbally ignore an order to return to the staging area, where a certain Super Prototype knightmare frame, the one and only Lancelot, was waiting for a pilot. Later, with the original choice of pilot a no-show, Suzaku Kururugi gets to answer the call instead. Given how everything worked out for the two of them, one has to wonder what could've been.
Kyle Rayner was explicitly chosen at random to be the last Green Lantern, but adapted very well and eventually rebuilt the GL Corps. However, the shadow of Hal Jordan always hung over him, as well as his randomly being empowered. With the later return from the dead of Hal Jordan, Kyle felt that he was now replaced by the "true" Green Lantern of Earth. Admittedly, Hal took over for him in the GL comic, but Kyle got a massive power up and his own limited series.
In a more direct example of the trope, it is revealed at one point that the ring Hal Jordan received could have gone to either him or Guy Gardner. Hal was chosen because he was physically closer. Guy would later receive his own call.
It was later revealed that the ring chose Clark Kent first, but the Guardians of Oa ordered it to ignore him. They really, really hate Kryptonians, and now, generally act like Jerkasses to Superman.
Ironically, Kyle Rayner is widely considered the greatest Green Lantern BECAUSE he was chosen at random. Hal and Stewart were both military men (With Gardner a former cop in the new 52 and raised in a rough home prior to), so both were naturally capable of not being afraid, (thus not making them prepared when they are overcome by it.). Contrast to Kyle,who as an artist, is subject to he worry and fear of his work coming under scrutiny and criticism. As such, he accepts his fear and understands terror and started the trend of having Green Lanterns overcome their fear rather simply not being afraid.
In the Top Cow Productions comic book series Freshmen, Norrin, the only member of the team who wanted to be a superhero was out for pizza when the Applied Phlebotinum exploded and gave everyone else superpowers. He takes it fairly well and becomes the team leader and resident Badass Normal.
X-Men has a villain version: It was revealed that Charles Xavier, not Cain Marko, was actually intended to get the Ruby of Cyttorak and become the Juggernaut, but as luck would have it, Cain was really, really good at being Juggie in the end, so the demon Cyttorak didn't make a fuss... until Jug's Heel-Face Turn.
The premise of the comic book Major Bummer: the Imported Alien Phlebotinum that gave uber-slacker Lou Martin his powers was intended for uber-samaritan Martin Louis, but the alien who left it on Lou's doorstep didn't realize that the phone book prints last names first. Since the phlebotinum can't be removed without a fatal surgical procedure, Lou's stuck with his powers, but for the entire length of the series, he tries his hardest to maintain his slacker lifestyle. Unfortunately, the plot keeps finding him.
Lampshaded in Ultimate Spider-Man when the genetically modified spider flew off Peter Parker's hand after biting him and lands on MJ's chest, before being knocked to the ground and stomped on. When MJ finds out that Peter is Spider-Man, she exclaims that "I could'a been Spider-Man too".
In the future setting of Fray, the demons that plague the buffyverse were largely evicted years ago, leading to the weakening of the slayer lineage. Cue the return of the vampires, and the calling of Mekala Fray who has the strength, agility and speed of a Slayer but none of the dreams and memories of those who came before her. Turns out it had all gone to her twin brother, Harth, who was turned and became the Big Bad.
In Game TheoryNanoha's mother Momoko has significant magical talent, but because she grew up on Earth, where there's no knowledge of magic, she never got a chance to use it. Although that's changed recently.
Nearly happens to Brian in Monty Python's Life of Brian, when the wise men come to the wrong stable. Luckily, they realise the Messiah they were looking for is just down the road. Though they have to get their gifts back.
Subverted in The Matrix. Neo asks the Oracle if he is the one, and she replies "Sorry, kid, maybe in your next life." After Morpheus gets nabbed by the Agents, Neo says Screw Destiny and goes to confront the agents and free Morpheus even knowing he's not The One. The reveal is that he just needed to decide he was The One to become The One.
In the 2010 Alice in Wonderland movie has Absalom declare Alice to be "not hardly" the Alice they're looking for. Later, Absalom tells Alice that at the time, she was "not hardly" Alice; by the time they meet again, she's "almost" become Alice.
One interpretation of his statements, that all the other characters miss, is that she is not the Alice shown on the scroll because it is not yet the Frabjous Day.
This trope functions as the center point of Shrek 2, as Prince Charming shows up to woo Princess Fiona as part of his role as the hero, but instead finds out that Shrek had saved her during the events of the first film. This causes the catastrophe of events that follow in the sequel.
Cats & Dogs: The Big Bad manages to abduct Buddy, the dog agent posing as the Brody family's pet (he's fine). The dogs need a new agent in place immediately, and when Mrs. Brody goes to a farm to find a new puppy, Dog Intelligence has replaced the existing litter with handpicked new recruits. However, Lou's quest for adventure kept him away from the switchout, and he ends up being picked over the recruits.
Sir Apropos of Nothing, of the series of the same name, collects a lot of missed calls. He's not at all happy about it.
Neville Longbottom in Harry Potter: Both Harry and Neville fit the conditions of the prophecy of the one who would defeat Voldemort, but Voldemort unknowingly made Harry The Chosen One by "marking him as his equal." Harry suspects the other could still be the one to defeat Voldemort, but he is shot down by Dumbledore saying that while Neville may once have been a candidate, he is no longer, as Voldemort chose Harry. That's what happens when you go by half a prophecy.
In Orson Scott Card's Homecoming series, younger brother Nafai outright asks The Oversoul whether he was the first choice to receive the Cloak of the Starmaster. The Oversoul admits that Nafai's elder brother Elemak was the first and natural choice, but he was also an incurably bullying Jerk Ass. So The Oversoul went with Plan B, rather than risk Elemak simply refusing to get with the program.
No, Nafai assumes he was plan B, but the Oversoul tells him "Elemak is far more crippled than Issib." If Elemak wasn't an arrogant Jerkass, he probably would've been plan A—but he was, so he wasn't.
In The Westing Game, Sydelle Pulaski is noted as being the only heir with no connection to Sam Westing. This is discovered to have been because she was never supposed to have been an heir in the first place. The invitation to the game she got was actually supposed to have gone to a Sybil Pulaski who was friends with Westing's wife.
In the Dragonriders of Pern novel The Skies of Pern, it's said in T'lion's backstory that he was never meant to Impress his bronze, Gadareth — his brother was the actual candidate — and though his brother, K'din, Impressed a brown, to K'din, his little brother — who was barely old enough to be a candidate — Impressing a dragon of a higher rank was completely unforgivable.
During the story arc of the three, Jayfeather believes that Hollyleaf is the third cat because he and Lionblaze are two of the chosen cats and she's their sister. As it turns out, Hollyleaf was completely normal and the real third wasn't even born yet.
Also, in the second arc, the Tribe thinks Stormfur is the chosen "cat with a silver pelt" who was going to save them from Sharptooth because the real silver-pelted chosen one was covered in mud at the time, hiding her fur color.
In Holly Lisle's Minerva Wakes, Minerva and her husband were sold wedding rings that were supposed to wake their innate magical abilities and turn them into magical guardians who stand against the Unweaver. When this is finally explained to her, Minerva is startled but ready to step up and meet her destiny; she's less than thrilled when it is further explained that the people who were supposed to get the rings showed up half an hour later.
A variation happens in Buffy the Vampire Slayer, seventh season. Dawn and everyone else believes she's been chosen as one of the Potential Slayers, due to Willow's location spell seeming to aim right for her. Unfortunately, she later finds out it was in fact aimed at the girl behind her, behind the door, in fact, just outside the house. The spell also frightens the girl, causing her to run away, further delaying the reveal. She takes it remarkably well, considering her history. Almost... heroically well.
On The Middleman, Wendy happens to run into Tyler, who it turns out was another candidate considered to become the Middleman's sidekick. As luck would have it, he missed the call: his roommate forgot to give him a phone message, and by the time he got it Wendy had the job.
In Kaamelott, King Arthur seems to be The Chosen One: he is the only one who can pull Excalibur out of the stone, and Excalibur only glows when Arhur wields it. But it is later revealed that Excalibur glows even brighter when Percival wields it, and Lancelot was the first choice of the Gods. When Arthur puts back Excalibur into the stone so that everybody can try to become the new king, they both don't try. Perceval refuses to try it because he is loyal to Arthur, and Lancelot is hiding in a remote location.
Very nearly happened all the way back in The Bible: Samuel knows he must anoint one of the sons of Jesse as the next king. The first son he sees looks every inch a king to him. His name? Eliab. Samuel goes to give him the king makeover, only to be told by God that it isn't Eliab he's after... it's David.
There was actually quite a number of sons and all but one of them were gathered in the house because they were apparently that impressive. The runt of the litter (David) was outdoors tending sheep.
You could argue it was played Straight with Saul, except it's repeatedly made clear God rejected him for what the did after being Chosen, and he's still considered the LORD's anointed.
Then there was that whole Jacob-Esau mess. Esau eventually mellows.
During the Metru Nui storyline of BIONICLE, the Toa Metru learned that they only became Toa because the Big Bad Makuta interfered with the Call, directing it away from the intended recipients. Ultimately subverted, as it was a Kansas City Shuffle by the Hero Secret Service: Makuta was going to make dang sure someone Missed The Call, so fake targets were set up to be passed over in favor of the real heroes.
This is first seen when Sora finally catches up to Riku and shows him the Keyblade. Riku is able to take it from Sora effortlessly, and Sora can't call it back (though it's a humorous moment that doesn't seem important at the time). Riku is a good sport, so he gives it back. Later at the Hollow Bastion Riku takes it from Sora by force to aid Maleficent. Sora has to fight through the Bastion without the Keyblade and without Donald and Goofy until he duels with Riku.
The second game subverts this by saying there is no 'The' Keyblade, instead anyone with the right qualifications can have a Keyblade. No fewer than nine Keyblade users have been shown (Sora, Riku, Mickey Mouse, Roxas, Xion, Kairi, Terra, Ven, and Aqua).
There is also Eraqus, Yensid, and Xehanort before he lost his memories as well as well as whole armies of Keyblade wielders in the past. It's also mentioned that there are many more currently active keyblade users that are scattered throughout the realms as well.
Not to mention Lea (Axel's Somebody) reveals that he is able to use a keyblade at the end of Dream Drop Distance.
In the first .hack game, the Twilight Bracelet was supposed to go to Kite's friend Orca. In fact, it did, but a minion of the Big Bad took Orca out before he knew how to use it.
Little known RPG Guardians Crusade actually does this twice. First with the adventuring party of Kalkanor, who clad in white armor usually tends to defeat or at least weaken all major bosses before you arrive and generally act as the hero of the tale, until he is betrayed. Second is Darkbeat, whom most everyone in the game assumes is the real hero after all, and sends you off to gather the Holy Equipment in his place. He didn't know that gathering the equipment was the test after all.
Dan from Street Fighter got a most literal taste of this. During the events of the Alpha Story Arc, Dan befriended Blanka, who was in the Street Fighter II games, while Dan was not. With his emergence in Street Fighter IV, Dan's absence from the II games was explained as such: Blanka did try to call him, but Dan had his phone cut after he hadn't pay his phone bill.
In Magi-Nation, Tony Jones is originally hailed as the hero and the only one who can stop the Shadow Geysers, until it turns out that maybe it was his presence that caused them to appear in the first place. Oops.
The main character to The Longest Journey series April Ryan practically defines this trope. She spends the game begrudgingly sacrificing everything by fulfilling one prophecy after another to prove that she's next in line to be the Guardian who will watch over the universe for the next 1,000 years. She's even told so by several people who know what they're talking about. But it's revealed that she's not actually the Guardian at all. The true Guardian was the villain April just fixed. April ends the game having given up everything because destiny told her to and having no purpose to her life after all. Talk about a downer.
Roger Wilco from Space Quest seems to qualify, according to the Companion. Captain Quirk was intending accomplish every single heroic task that Roger achieved himself since Space Quest 1, and now hates him for it. Near the end of Space Quest 5, he still fails and turns into the game's Big Bad
Subverted in Fate/stay night. Shirou ends up with the gamebreaking Saber, the best Servant in the Holy Grail War (except she's not as strong as she should be) out of a sheer fluke when Tohsaka had previously been setting up a ritual in a very careful manner in order to get said hero class. Instead, she got Archer because her timing was an hour off. But then it turns out Tohsaka was going to get Archer no matter what due to the pendant he has and Shirou could never hope to summon another Servant other than that very Saber due to having her sword's sheath inside his body.
And according to some theories, Tohsaka was trying to summon the most powerful Servant in her current cycle. Archer is probably the strongest Servant, despite several of the other ones being outright breaking the game.
Though near the end of the series it is revealed that they went on a different adventure of unspecified details. We're told that it involved other dimensions, but beyond that, it's never made clear.
Captain SNES: The Game Masta suggests that Ryan was originally supposed to be the Game Master, but Alex ("Second best Captain SNES") ended up filling the role instead. The reasons why are not entirely clear, but it's fairly clear that the certified perfectly ordinary cat was somehow involved.
In Guilded Age, Payet Best fulfills almost all the requirements of a prophecy made by a mad woman in the town and is declared the "Epic Hero". The real Epic Hero (who fulfills the one requirement Payet missed) shows up after a few days, but the mad woman has a heart attack right after due to the strain of shouting "THE PROPHECY!" over and over.
In The Drunk Duck webcomic The Wrong Hero, a top hat wearing cat ends up 'waking' the wrong man. It's too late for the right guy as his house explodes, so Simon (the titular Wrong Hero) is stuck with it, whatever it is...
This is the premise of the Footloose sub-comic Cherry: Origins of a Magical Boy. Steve Lewis is standing ( in drag ) on the sidewalk, when the opportunity to be a magical girl drops from the sky, just barely missing the girl it was probably intended for. Steve decides to take on the role. He's straight, by the way.
Harrison the Shark of Nedroid constantly pines away to be swept up in some big heroic adventure like Beartato and Reginald often are. He's offered several chances practically on a silver platter, but turns his nose up at all of them until recently. Then he comes across Beartatonote Well, actually just a Beartato doppelganger and Reginald, who fell into the same thing he was chosen to do.
In Spacetrawler, the alien Nogg uses a powerful computer to find the six humans most likely to help him on his mission. One of them, Bill Landing, is located in Australia. Nogg swoops down to Bill's address, stuns the guy who matches the picture, then leaves with his newest "volunteer". After getting too far to turn back, Nogg realizes he grabbed Bill's brother, Dustin, by mistake. Dustin, of course, wants nothing to do with the mission, and is little more than a thorn in his shipmates' sides for the rest of the adventure.
Nara of JourneyQuest seems to feel like this about the Sword of Fighting going to Perf instead of her.
And in the early second-season Alternate Universe episode Gwen 10, it's Ben who misses the call. He gets a Peggy Sue back to the start of the series and inadvertently screws things up by knowing too much... causing Gwen to be the one who winds up with the Omnitrix. Ironically, the episode ends with the Omnitrix attached to Grandpa Max after Vilgax removes it from Gwen.
Somehow, The Fairly OddParents plays this straight, lampshades it, then subverts it in the Wishology Trilogy. Played straight at the end of Part 1, where Turbo Thunder is revealed to have been the one apparently chosen. This is lampshaded throughout most of part two, mostly by Timmy trying to send the bad guys after Turbo Thunder instead; then subverted near the end, when it turns out that Timmy really is the chosen one.
Kim Possible's first adventure was in response to a call intended for Team Impossible, a group of heroes for hire. In one episode, Team Impossible, annoyed that her helping people free of charge cuts into their business, tries to force her to quit.
A brilliant one in Archie's Weird Mysteries that combines with a Prophecy Twist. In the three-part vampire arc has Veronica as the ender of a Vampire Lord after Archie's guess that a girl called Scarlet is the one seems to be wrong. As it turns out despite being a vampire and a loyal servant of the Vampire Lord, Scarlet was the true ender and Archie was right all along. A line from the prophesy was misinterpreted:
Veronica: "Raven and red upon their heads. Destiny awakens. One girl is the ender. While another is mistaken."