One opponent in Flame of Recca's Tournament Arc managed to temporarily steal Recca's ability to summon his flame dragons. Setsuna, already a saucy and rather disobedient dragon, promptly asks why the hell he should listen to some new guy and fried him in annoyance.
In Dragon Ball Z, Quirky Mini Boss Squad leader Captain Ginyu trades bodies with Goku. This is fairly ingenious, because he waited until he was weakened and nearly defeated by Goku before trading. To make it even better, he inflicted a severe wound to his own body (punching himself through the chest) immediately before making the switch. However, he couldn't get full power out of Goku's body, because he doesn't know his powerup technique, the Kaio-ken. Unfortunately for him, Vegeta then shows up and beats the snot out of him before he gets it to work.
When Pist from Final Fantasy: Unlimited steals Kaze's Magun, the device that allows him to summon powerful being using special bullets, he tries to use it himself (including a bizarre subversion of the normal firing sequence) but the resulting summon turns on him.
The rambunctious Kamina steals the Gurren and, confident that he has access to new powers, attempts to combine with the Lagann as the head. It fails pathetically and hilariously. They eventually get it to work through determination.
Similarly, Simon has a few issues with Lagann's systems at first, especially the jet thruster. Quoth Yoko: "Ah, hello? We're sorta falling..."
In Code Geass Lelouch instinctively knows the basic principle behind the Geass but not all of the specific rules. For example, when he first gains the Geass power, he knows it can be used to force a group of people to obey any command he gives, even taking their own lives, but when Viletta confronted him in her Knightmare, he found out the hard way that he needed direct eye contact for his power to work. Similarly, he does not realize that he cannot use the Geass more than once on the same person until he makes the mistake of trying to use it on Kallen twice. After this second mishap he uses logical, scientific methods to deduce all of the possible applications and restrictions of his new ability — such as commanding a girl to make a mark on a wall every day to see how long the effect of his Geass takes to wear off. Turns out, it doesn't wear off. Ever. Word of God says she went back to Britannia after Season 1 and her attempts to get back to Japan and mark the wall are interpreted as sleepwalking thanks to the time zone difference. The fifth episode shows just how Crazy-Prepared he is by having him rattle off all the things he's learned via experimentation, such as its maximum effective range of 270 meters. The audio commentary lampshades this when the voice actors (including Lelouch's) muse on exactly how he discovered these things, suggesting (for the range example) that he used cell phones in walkie-talkie fashion.
There's a sequence involving Light Yagami learning the rules and limitations of the Death Note before he embarks on his great scheme of moral cleansing. He continues to experiment with its powers and devise loopholes throughout the series. By the end of episode three, he know more about the thing than Ryuk, a shinigami.
The Yotsuba executives (or rather, just Higuchi) also learn some of its rules this way, for instance, giving someone a death condition that is physically impossible will result in that person simply dying of a heart attack.
In Gate Keepers, Ukiya Shun is blessed by the Gate of Wind. It took him several episodes just to properly summon the power again (which he did in the first episode by accident), and an episode testing a new technique (which he later perfects).
The manga has Tsukune kidnapped by a shapeshifter, who copies his form and goes out to fight Tsukune's Unwanted Harem. Unfortunately, the fellow runs into quite a few How Do I Shot Web? moments as he tries (in vain) to kill them, not realizing that he's far, far weaker than they are in human form. When he wises up and copies Moka's Superpowered Evil Side, he's beaten for good when the power of the rosary weakens him.
Tsukune himself had a bit of trouble until he got some well-earned training with Inner-Moka and Touhou Fuhai.
Sort of happens to the protagonist of Pretear, Himeno Awayuki — more of "How Do I Shot Wind?" It is implied that she should know instinctively how her powers work, but the first time she is forced to fight a monster, she panics and can't figure out what to do. However, this wasn't enough to make her give up, and she actually demands to receive some training in order to learn to use her powers properly.
Skuld gets this in Ah! My Goddess when she tries to develop her water powers. It doesn't work out, and she puts herself in danger by trying to accelerate things; this danger being caused by her proclivity for Tim Taylor Technology.
In Fullmetal Alchemist, Ed instinctively knows that he can do transmute without a circle, what with having seen the Truth and all. This fits in with how he was able to bond Al's soul to a suit of armor immediately after losing his leg, when alchemists who had devoted years of research to it had far less luck with human transmutation.
In the 2003 anime version, Ed instead learns of this ability by clasping his hands in frustration then grabbing a basin of water, heating it through alchemy to boiling temperature. Afterward, he has no clue how he managed to do it, and his attempts to reproduce the effect are unsuccessful until he finds himself in another emergency situation.
Ichigo Kurosaki accidentally sets off his Getsuga Tenshou attack immediately following his achievement of Shikai. He doesn't learn how to fire it at will until he reaches Bankai. Much plot with Ichigo concerns the fact he has great power, but no real clue how to control it. His sword is mocked explicitly for being a "Big ball of fluff".
It got even worse when Ichigo unlocked his Fullbring. At least with a sword you know that the basic goal is to stick the stabby end into the bad people, but how the heck are you supposed to fight with a giant glowing swastika?
And now yet another ability has come out in this way. Ichigo's about to get his throat carved out, and suddenly manifests Blut Vene... a Quincy defensive technique that blocks the attack. Ichigo not only has no idea how he did this, he didn't even realize that he had done anything at all until the bad guy pointed it out.
Making things even worse, Ichigo had a Power Limiter or three he didn't know about, most of which were operating sporadically. So trial and error wasn't a reliable method of figuring out what he could do or how, either.
Chad and Orihime aren't exceptions, either. They have to learn how to summon their powers at will (with fairly amusing results at first, especially when Chad tries to remember what Ichigo's younger sister Karin looks like), although Orihime manages to improve to the point where she can use her Shun Shun Rikka without calling their names. In the Bount Arc, Uryu has these issues with the artifact that he uses to fight without his powers.
Part of the reason for Renji's loss against Byakuya is that he didn't know how to control his Bankai, enabling Byakuya to disrupt its rhythm and leave him vulnerable. Byakuya claims that mastering bankai takes at least ten years of training. Something that he has, and Renji (who had just achieved bankai that day) lacks.
Whenever they figured out a new thing the ship could do, trying it always lead to embarrassing mistakes. The first time they tried to take off, the anti-grav units broke free of the ship. Using the fold system left them millions of miles off-course, surrounded by inhabited bits of the island they folded near, and the fold engine disappeared. The first time they transformed the Macross, they destroyed the entire city inside the ship. The first time they fired up an impenetrable energy shield, the shield generator overloaded and destroyed Toronto. Though they were able to use that last one to take down Boddolza's flagship by using the Daedalus Maneuver to break through the hull and then activate the shield while inside. It nearly destroyed the ship, but it's still the ship's and crew's Crowning Moment of Awesome.
Humorously, this is also why they survived so long against the Zentraedi attacks: whenever they pulled one of these stunts, the Zentraedi commanders were unsure of whether the humans meant to do that or not, and therefore wonder what other tricks they must have up their sleeves, leading to an overly-cautious approach on their part.
On a much smaller scale, Hikaru in the second episode is a very competent pilot... of airplanes. When his Valkyrie unexpectedly turns into a giant robot, he promptly tries to make it walk. He topples forward and wrecks Minmay's room in doing so, and needs a conveniently-passing-by seafood truck to right him again.
Macross Frontier has an excellent deconstruction of this trope. Sheryl Nome received some basic training on how to operate a VF-25; when the time came to put it to the test, her eyes narrow and she even gets a Theme Music Power-Up, which lasts long into her glorious failure at even flying in a straight line.
In Zatch Bell!, almost every time Zatch and Kiyomaro learn a new spell, Kiyomaro still struggles to understand that the spells are powered by emotion and will. However when they learn their third spell, which magnetizes their opponent, Kiyomaro tries several unsuccessful attempts to test this spell (which he didn't know the effects of at the time), and eventually tried singing the incantation, very badly. Part of the punchline with the third spell was that he was casting it successful in his tests, just that since the spell is purely magnetic and he tested in a place with no metal around, the spell had nothing to effect. Happens again with the fourth spell as despite putting in emotion, the spell didn't work. They later learn that instead that spell works off of tension rather than will. Eventually Averted when Kiyomaro dies and obtains Answer Talker, allowing him to know literally everything. And then used again when it turns out he doesn't even know how to control it yet, needing help from Dufaux just to get it to work.
In YuYu Hakusho, as Kuwabara is trapped inside Mitarai's water monster, he is determined to break free, and suddenly summons a special sword from his spiritual energy that can slice through dimensions, freeing himself and his friends and defeating Mitarai. The next morning, he tries to summon the same sword while fighting Sensui, but ends up getting his normal spirit sword instead.
Nami with the Clima-Tact in her fight with Miss Doublefinger. Unfortunately for her, half of the functions on the device are party tricks (and they're listed first in the instruction manual), and the other half are abilities that are useful, but only if used correctly, and Usopp may not have known how good they can be (he suggests playing boomerang catch with the Cyclone Tempo). Despite this, once she manages to find the right functions to use, she can win if she identifies the good moves and learns how to use them. Nami's experience with the Perfect Clima-Tact is also like this to some extent, but only because she didn't realize how powerful it was the first time she used it.
This applies even more to the Devil Fruits. The average person who has absolutely no idea what their fruit even does unless they've either read a restricted access catalogue or been outright told. Even then, you'd have no idea how to activate it until you experiment. Brook's power only activated after he died, meaning he could've started off simply knowing he couldn't swim. Hell, Brook takes this even further after the Time Skip, when he develops his powers into the abilities to use Astral Projection and channel Ghostly Chill into Ice Powers. This means that it took Brook well over fifty-two years to realize these powers were available to him and work out how to use them.
A flashback to Luffy's youth showed that it was years before he could even use Gum-Gum Pistol (basically just a stretching-arm punch, which is Luffy's most basic attack in the main storyline) without hitting the ground or it rebound into his own face. Though that can be largely blamed on his youth and his relatively small body at the time.
After Kaku ate a Devil Fruit that transformed him into a giraffe or giraffe-man hybrid, he had trouble changing into the specific form he wanted and, since he hadn't been able to explore his new capabilities, just made new attacks up as he went along. Even so, he was a formidable opponent and adapted to his new powers much faster than the average DF user. Still, having a full-grown giraffe fall through the ceiling made for some hilarious moments.
Tashigi, after she was body-switched with Smoker, has a hard time using the latter's Devil Fruit powers, and has to ask how to use them.
Momonosuke also has a hard time figuring out how to control his transformations into a dragon and back after he ate an artificial Zoan-type Devil Fruit. Though in his defense, it could be either due to his young age, his inexperience with the fruit (And limited knowledge of Devil Fruits in general), the fact that said fruit is artificial and a failure, or all of the above.
Sabo had some issues with controlling the abilities of the Flame-Flame Fruit after first eating it. While he was able to utilize its previous user's signature technique, he had trouble turning off the flames. Also, despite the Devil Fruit being a Logia and giving him "Made of Air" style Nigh-Invulnerability, he still dodged attacks simply out of habit.
Trafalgar Law's Op-Op Fruit abilities make him a borderline Reality Warper, but at the time he first ate the fruit he had no idea how to actually use its powers. Thus he was unable to help Corazon/Rocinante after the latter was riddled with bullets.
In Sound Stage 3 of Magical Girl Lyrical Nanoha Striker S, Teana, having had the fourth and final stage of her device limiter removed, has a new long-range mode for Cross Mirage, but decides to work on the skills she has since there won't be enough time to master it before the final battle.
In an episode of G Gundam, a disgruntled fanboy steals Domon's Gundam believing that he can pilot it better. However, things go awry when he doesn't know how to properly operate the Gundam, requiring Domon to come and save him. It isn't "proper operation" so much as "any sort of physical training" — the suit-up process is shown to be quite painful, even to a trained martial artist like Domon, so the preteen boy nearly broke several bones before Domon hit the abort.
Amuro and Garrod's first sortie was "Use vulcans and scare off my enemies and tank the machine gun rounds" and then "use sword to fend off enemy mobile suits". It was only after the first battle did they got the knowledge to pilot the suit. For Garrod's first experience firing the Wave Motion Gun, it gives Tifa a Heroic BSOD. Lucky for them that Amuro has Psychic Powers and Garrod is a genius at improvisation.
Kou Uraki of Mobile Suit Gundam 0083: Stardust Memory was just a rookie using a captured Zaku II for testing when he's forced to take up the GP-01. His inexperience with everything leads him to getting the GP-01 getting shot up when he takes it out into space without it modified for space combat.
Judau Ashta of Gundam ZZ had even less luck, despite his own considerable Psychic Powers: his first experience flying a Gundam mainly involved him clumsily crashing into things and defeating his opponent by sheer luck. Likewise Elle, who could only figure out how to move the Gundam's arms her first time, let alone make it walk or fight.
Tobia Arronax of Crossbone Gundam specifically has a Worker MS license, but this isn't much help in a Combat MS. In his first sortie, he expects to only be an extra turret, and his Batara flounders around a little before righting (it ends with Seaboo-, er, Kincaid bisecting it). In his second, some time after the first, he's in over his head and has to eject so Kincaid can take over. In his third, he survives largely because Barnes doesn't want to kill him. Then they give him a Pez Batara and he uses a Bit as a stepping stone, at which point his future Ace Pilot status is all but confirmed.
Seabook Arno of Mobile Suit Gundam F91 suffers from this for a bit as the only reason he pilots the titular MS is because his mother took part in its construction and he had a licence to pilot. He gets better. Much better.
Neon Genesis Evangelion: The first time Shinji Ikari tries to pilot an Eva with no training or preparation, he falls on his face. Fortunately, putting him in danger this way activates the Crazy-Protective Alter-Ego of his Eva suit, who handily defeats the Angel for him.
Season Three Katekyo Hitman Reborn! spoiler'd example: In the Future, when Tsuna first uses his Kill It with Fire X-Burner Attack, he can't find out how to set it off without propelling himself backward into a wall. When he figures out to use his other hand to make a balancing fireball, he THEN has the limitation that he can only fire on level ground, when he gets around THAT, he needs a way to balance out the flames. Luckily, we're spared that Training episode by Spanner.
Karin from Kamichama Karin wore the Goddess Ring for YEARS without having a clue that it could allow her to transform into a Physical God. And even when she finds out, she struggles long and hard before even being able to transform without help, much less be any kind of useful. It probably doesn't help that she's really, really stupid.
In Harukanaru Toki no Naka de - Hachiyou Shou episode 4, Tenma's attempt to protect Akane from Akuram results in him activating his Hachiyou powers for the first time, nearly frying Akuram with lightning. Tenma is clearly surprised by this ability, but when he tries to repeat this move on purpose a few minutes later, it doesn't work. In the next episode, he complains about the Hachiyou powers being useless due to not working when they are needed.
Naruto faces this difficulty with controlling the Kyuubi's chakra throughout the series. After the time skip it's largely a matter of not going berserk while using it, but pre-time skip his major problem is accessing the power to begin with. This led to a month of humiliating "training" in summoning tadpoles, culminating with being thrown into a ravine. And just to make it worse, when summoning really counts, he's only able to get a toad the size of his hand. Twice! Course at the time Orochimaru had hit him with a sealing spell which was throwing his Chakra out of balance. By the time Jiraya had removed that handicap, it was only a few days before Naruto had to fight in the second Chunin tournament, so he really didn't have any time to master it.
Inu-Yasha didn't even knew about Tetsusaiga'sKaze no Kizu / Wind Scar when he first got it. It took some time until he learned about it, more time to use it accidentally, even more time to use it at will and even more time to truly master it. When he gains a new power in his sword, he has to learn how to use it. Like the Wind Scar, the Dragon-Scale Tessaiga was something he struggled desperately to master and, in both situations, something his brother said was what started him on the road to mastering the power (in the case of the Wind Scar, his brother's help was accidental, in the case of the Dragon-Scale, his brother's help was deliberate, if not cryptic). In both cases, the main lesson for Inuyasha wasn't what the powers could do (which only had limited functionality) but what he could achieve when he believed in himself as a half-demon.
Sesshoumaru has the ability to instantly master any weapon, especially swords. He even knows how to master swords he hasn't even touched (such as Inuyasha's Dragon-Scale Tessaiga). However, when Tenseiga gained the Meidou Zangetsuha power, Sesshoumaru struggled to master the ability. When he did finally master the ability (after a humiliating encounter with an old enemy of his father), he realized that he wasn't meant to keep the power and passed it on to Inuyasha instead. It was the only sword power in the entire story that required a compassionate heart to master instead of fighting/weapon skill or instinct, and the lesson for Sesshoumaru was that he should never wield a sword without feeling fear at the possibility of losing loved ones or without feeling compassion for even his enemies.
In the original Mazinger Z manga, Kouji can't control Mazinger-Z when he first gets it and is forced to have Sayaka run out in the Aphrodite A to stop him and get him under control. The Mazinkaiser OVA takes it one step further: Kouji thinks he can control it, but it takes control of him then goes into a berserker rage.
Unlike virtually every other Precure before her, Tsubomi Hanasaki, alias Cure Blossom, of HeartCatch Pretty Cure! has to be practically hand-held through most of her powers and abilities early on. Compare this to her teammate Erika Kurumi, alias Cure Marine, who was able to figure out everything on the word "go".
A similar situation happens in Smile Pretty Cure! with Miyuki Hoshizora, alias Cure Happy, though she's quicker mastering her powers than Tsubomi. And once she does, cue the pink heart-shaped Kamehameha. Though, it's starting to seem like the rest of Miyuki's teammates are stuck in this same predicament.
Inazuma Eleven has this: Endou's Seigi no Tekken and God Catch, Tachimukai's Majin the Hand and Mugen the Hand, and Kidou/Fudou's attempt to create Emperor Penguin No.3.
Beet the Vandel Buster started off with the five ultimate weapons given to him by his dying heroes. Of course, he still had to learn how to use them, and after several years was only able to use one, the spear, effectively. He eventually learns to fire more than one shot with the gun, and comes closer to mastering the shield with training from its original owner (who was Not Quite Dead). With foresight he learned to work around the axe's twelve-second materialization time, and over time got better at the sword bit by bit if nowhere near able to master it. In fact, when the series was cut short at twelve volumes, Beet still arguably hadn't totally mastered any of his weapons!
In Pokémon, occasionally one of the heroes' Pokemon will have trouble mastering a new attack until several episodes later. One of the Sinnoh arc's running gags was Gible's Draco Meteor misfires always homing in on Piplup.
Then there was Duplica's Ditto, which couldn't master transformations for a long time...it would never get the face right.
In Omamori Himari, Himari and other characters are confused as to why Yuuto's powers have not awakened when he turned 16 like they were supposed to. Later, he uses them by instinct during a life-or-death situation. The next episode has him trying to train to use them at will, which doesn't go anywhere. It is triggered by his will to protect others. Later on in the manga it's explained that the Twelve Families traditionally only passed on the knowledge of how their powers work through oral tradition, and since Yuuto's family didn't teach him the family secrets before they died, he honestly has no clue how the Light Ferry works, and there's nothing and no one he can consult for lessons. He has to rediscover all his family's techniques from scratch.
In The Familiar of Zero, the reason why Louise seems to be an Inept Mage is because her affinity is Void Magic, a long forgotten art. Once she learns this, she becomes much more effective when she figures out the kinks. Saito's power is to become an Instant Expert with any weapon, but it takes him a while to realize that it only works with real weapons. He tries to use an ornamental sword and gets his ass kicked. He also needs to be in a real fight, as when he tried to twirl a sword around to show off, he made a fool of himself.
Above example is anime only. In the original light novels, Saito is capable of wielding the ornamental weapon as if it were any other and the activation of his abilities was merely dependent on being in contact with a weapon. The ornamental weapon was still meant to be a weapon, it just broke the first time Saito used it because it wasn't durable enough to withstand being used to strike stone by someone of Saito's strength. The trope is still played straight with Saito's combat abilities, though. He can swing a sword like a natural and gains incredible speed and strength, but it takes him some time and a fair bit of practice to be able to fully get a good head for actual combat.
Touma Kamijou has no idea how ImagineBreaker works. Throughout the series, he slowly learns its limitations, and eventually figures out how to pull a Catch and Return with it. To be fair to Touma, almost nobody knows how Imagine Breaker works. Aleister Crowley is the only one who has hinted that he knows how it really works (and he has no particular desire to explain it to anybody else).
Later deconstructed when Othinus reaches her full power and alters the world to her whims. Touma is the only one unaffected and knows Imagine Breaker can change the world back, but is unable to figure out how. Fortunately, he gets her to pull a Heel-Face Turn, and she is convinced to restore the world to the way it was.
Sogiita Gunha has a multitude of powers like Super Strength, Super Speed, teleportation, force fields, etc. While he knows how to use them, he has no understanding of the science behind them. It is pointed out that he would become much more effective if he knew how his powers worked and took better advantage of them. This is unlikely to happen as Gunha is an Idiot Hero who lives by Honor Before Reason and guts alone and has no interest in brainy topics.
Kouya's Garuda Eagle from Crush Gear Turbo was once the Gear of Kouya's deceased elder brother, who happens to be the World Champion. Apparently, said Gear has a very powerful super move. Unlocking the secret involved several episodes of having the Gear analyzed by an ultra-powerful supercomputer just to learn the underlying science for the super move, and another batch of episodes of Kouya trying to find the right conditions to use the technique, and use it reliably. Even better, the supercomputer belonged to Kouya's wealthy rival Manganji who had his men surreptitiously copy a virtual data of Garuda Eagle, and said discovery of a special ability was a complete accident.
The Bird Men spend significant time learning the basics of how to fly, and for one particular character, it took a Die or Fly moment to learn it.
The main-line Spider-Man actually subverts the trope. Many of his powers are hardwired into his reflexes and instincts. As such, acrobatics, fighting, dodging bullets, and balancing are all things he can do automatically. In his introduction, he backflipped twenty feet and stuck to the side of a building mere minutes after being bitten by the radioactive spider, purely because his Spider-Sense sensed a car about to run him over. Even web-slinging needed little practice purely because his reflexes prevented him from screwing up. Spidey's biggest problem tends to be the fact that his opponents are stronger and faster than him and/or have an Instant Death Radius that requires him to be smart about using his powers.
Spidey also had no trouble figuring out how to shoot webs because it isn't actually one of his powers! That's right, Peter Parker actually designed some web fluid and shooters using his awesome powers of nerdiness. At least, not until the times in the comics when he (temporarily) does get natural webbing.
However, he did have a minor problem when his Spider-Sense got burnt out - without it, web-swinging was much more tougher as he has no way of knowing what's safe to swing on or not.
This trope is used occasionally in the Ultimate Spider-Man comic: most egregiously, when Peter Parker startles out of daydreams in school and breaks his desk multiple times without anyone becoming unduly suspicious about it. Public school chairs... The most hilarious use of this trope is when Wolverine and Spider-Man switch bodies. Wolverine's attempts to learn how to websling must be seen to be believed.
The new Spider-Man Miles Morales currently does not shoot web, but would really like to. He's asked Spider-Woman but she didn't answer him. He eventually receives his own web shooters, but it takes him a couple of tries before he gets the hang of swinging without smacking against a wall or onto a rooftop.
Spider-Girl didn't exactly have problems learning to use her powers, but she needed training from her father and his friend Phil Urich to really be able to master them and become a more experienced fighter.
Similarly, Phil Urich himself had a number of problems figuring out how to use the Green Goblin's equipment when he moonlighted as a superhero in the short-lived Green Goblin series Marvel published in the 1990s. Later, in Runaways, he knew how to fly the ship the mysterious benefactor gave Phil's group because it was based on the Goblin equipment.
Spider-Man's ally and generally lovable loser the Fabulous Frog-Man. Stealing the fully automated frog-suit of his father, the villainous Leapfrog, Eugene Patilio wholeheartedly attempts to make a difference while being utterly clueless about how the suit works. This proves to be his greatest strength, however, as his frequent misfired jumps tend to knock out waves of bad guys and make him look like a real hero who knows what he's doing. Pretty much the only person who knows that Eugene is a bumbler in person is Spidey himself.
The Super-Skrull is a recurring Fantastic Four villain who can use all the super-powers of that team, plus has a native alien ability to shapeshift. Nevertheless, he is always defeated, usually by the Four's ability to work as a team. It's been explain in canon that one of the reasons he loses to the FF is that some of them have gotten upgraded (either explicitly or via Power Drift) since he was created. For example Sue Richards wasn't the most powerful member of the team when they copied her, so her powers are stronger than the Super Skrull's. The Thing and Johnny Storm also had power ups. Reed has stayed the same, but his real power is his brain and he is indeed smarter than Super Skrull. It must be noted that Sue Storm's original power, that is, the one copied by Super Skrull, is the power to turn invisible (at the time, Sue was called "Invisible Girl"), which at the time was roughly the weakest, dumbest and most feeble excuse for a power in the Marvel universe. Her power upgrade (which Super Skrull does not have access to) is the ability to create invisible force fields of any shape or size at will. This upgrade ended up making her one of the single most powerful (and shitfire lethal) mortals in the Marvel universe. In other words, Super Skrull's stolen powers are one-fourth wildly obsolete.
Another factor is that no one understands the FF's powers better than the FF themselves, so they know exactly how to counter them. On the other hand, the Super-Skrull is shown to be extremely effective when fighting other enemies, since he's ruthless enough to use his powers in ways the FF never would, like stretching parts of his body into razor wire to decapitate enemy soldiers. Xavin, another Skrull with similar abilities, can barely use more than one power at a time. Although in the Secret Invasion tie-in, it was shown that while Xavin can only use one power at a time, he became better at using them individually than his teacher could. In Secret Invasion, it is revealed that the Skrulls now have the idea to copy any superhuman's powers, appearance, and memory perfectly. As revealed in the sub-series New Avengers. (written by the same dude), they really, really worked very, very hard at it.
The Justice League suffered a multiple bodyswap in the TPB Foreign Bodies; a female villain called Psykosis was incited to do it by Kobra. It ended up with Kyle Rayner (Green Lantern) operating the body of J'onn J'onzz, J'onn taking over Aquaman's body, Aquaman in temporary possession of Wonder Woman's body, Wonder Woman in Psykosis' body, Psykosis' psyche in Flash's body, Flash in Steel's body, and Steel in Green Lantern's body. Separate to this, Superman and Batman had simply swapped bodies or so it seemed; in actuality, Batman was indeed in Superman's body, but Kobra had taken command of Batman's body, leaving Superman resident in Kobra's body. And boy howdy, Hilarity did indeed Ensue at nearly everyone's expense before it was over. Worth noting that Batman gets an immediate grasp on Superman's powers, and starts saving the day worldwide. Only, he laments that so much power is distracting.
In JLA: Year One, everyone's powers (and their related body parts) are stolen by a villain. He seems to instantly know how to work each individual power, but the villain primarily relies on Green Lantern's ring, the flashiest and most "powerful" of the abilities. By overlooking the benefits of each different power Aquaman is able to overpower and kick his ass.
Subverted in the current origin story of the Hal Jordan Green Lantern, Emerald Dawn. In this story, Jordan stumbles about with his newly bestowed power ring, barely defeats a powerful villain and realizes that he is out of his depth with the weapon. To solve that problem, Jordan asks the ring if there is another member of the Green Lantern Corps he can talk to for help. The ring whisks him away to meet Tomar-Re, who recommends that Jordan come to GLC headquarters on the planet Oa for the optional training program. Jordan, naturally, takes that advice.
This appears to have been retconned somewhat in the new Secret Origin of Hal Jordan. Hal gets the ring and uses it to fly and make a few constructs without much difficulty, but is not aware of the full functional capacity of the ring. He is then forcibly brought to OA for mandatory training.
Was actually a major theme of the original 1960s X-Men, and still appears at times. It could easily be argued that this trope is the basis for the X-Men as a whole, as the series has always revolved around a group of mutants who are being trained in the use of their own powers at what is quite literally a school that exists for precisely that purpose.
Inverted with Rogue, who can use her powers quite well, but doesn't know how to turn them off (it's been pretty much spelled out that she could control them, except that some serious psychological trauma concerning both her power's first use and the effects of continued use were serving as a block.)
Subverted with Wing from Astonishing X-Men who tells Hisako (Armor) that after discovering that he could fly without propulsion, he assumed that this meant he was invincible as well and landed with a little too much force, breaking both of his legs.
An old X-Men villain was Mimic, a mutant who can copy up to 5 different mutants' powers. These powers become permanent if he can be around them for at least an hour. He was usually defeated due to three reasons; his copied powers were only 1/2 as strong as the original, he had no experience in using them, and he was kinda dumb. Eventually he got smarter (and did a Heel-Face Turn), and now has the original 5 X-Men's powers permanently (though only at the level of their teenage years; this is still formidable because he can use all 5 simultaneously, but it would've been downright game-breaking if he had the power-ups they've all gotten). He can also mimic an additional power on top of those 5, but trying more than that would be dangerous to him.
An AU Mimic becomes team leader in Exiles. This version had joined the X-Men and had spent years developing and mastering his plethora of powers and becoming a champion of mutants. His "main" powers for most of the comics run were Flight (Angel), Invulnerability (Colossus; couldn't fly in steel form), super agility (Beast), energy projection (Cyclops), and healing (Wolverine). Even with years of practice copying others Mimic admits that he wouldn't be stupid enough to try and copy a shapeshifter or teleporter for fear of accidentally killing himself.
The trope is very logically subverted in X-Factor when the team tracks down Alchemy, a mutant whose Puberty Superpower is the ability to transmute any matter into a simple element like gold. He was kidnapped by trolls and had to defend himself by transforming their leaders. He then couldn't change them back because he has to imagine the totality of the matter he is changing something into, and organic matter is so complex on a molecular level that he can't do it. So, he goes off for the advanced education in biochemistry needed to cure the beings he has affected.note One rather odd part of that story was that Alchemy refused to join X-Factor's school for mutants because it wasn't training in his powers but training in advanced organic chemistry that he needed. This was entirely true, but apparently the writers forgot that one of X-Factor's members was the most accomplished biochemist on Earth. By the time Alchemy reappeared in the pages of Excalibur, he had gotten enough education and control over his power that he was able to restore the humans he had inadvertently transformed after the trolls had kidnapped him again to try and force him to change their leaders back to normal.
Darkhawk received a cool amulet that turned him into an armored android with super-powers, but unfortunately it didn't come with an instruction manual. As a result, teenage Chris Powell ends up discovering many of his abilities by trial and error, and otherwise practicing to determine the limits of his abilities.
In an issue of The Avengers, the villain Absorbing Man absorbs the android Vision's ability to become intangible. He promptly falls through the pier he's standing on and into the water, due to a lack of control.
Liz Sherman from Hellboy can't control her fire powers at a young age, accidentally killing several people, including her parents. She joins the B.P.R.D. because they can teach her how to use her powers, or at the very least have ways to keep her from hurting people again.
Poor Empowered gains her powers from an alien supersuit that is the very definition of "enigmatic". She found out the obvious ones (Super Strength, vison enhancement, Hand Blast), but the other powers were discovered by accident. For example, her Wall Crawling was activated when she was thrown against a wall and she still hasn't actually "discovered" its flying abilities. It's Fanon (and suggested by Mind Screw in-universe) that the costume gives fantastic cosmic powers limited only by the user self-confidence. As Empowered has the self-confidence of a used kleenex in a dirty cesspool, you can see how it works. So yes, she unconsciously granted herself the power of being easily aroused and multi-orgasming. Kudos!
Speedball from the Marvel universe spent issue after issue trying to figure out how to get his bouncing powers under control; not just turning them off when they were inconvenient, but just bouncing in the right direction. He learned how just in time.
The Superman/Batman "Super/Bat" arc has a case where Silver Banshee "grant the wishes" of Batman and Superman (Superman to have a normal life, Batman to bring complete fear and order to Gotham's criminal underworld) by giving Superman's powers to Batman. It took Batman a lot of practice to use them right, and he realizes he needs sunlight to use them the best. Superman realizes that the side effect of Banshee's wish was both men did not have the means to properly use what they wished for.
Way back in Tales of Suspense #39, when Tony Stark first put on his first Iron Man armor to escape from a Vietnamese prison camp, he takes one step in his armor and falls flat on his face.
In Iron Man #200, Obadiah Stane puts on his brand-new baby, the Iron Monger suit, to fight Tony (wearing his brand-new Silver Centurion armor), because he knowsit's Tony coming after him. However, Stane has no experience, so he has to rely on a remote computer to assist him in the fight. When Stark realizes this (as he's been detecting strange transmissions throughout their fight), he destroys the building that's been transmitting to Stane's suit, leaving Stane outmatched.
Averted with Iron Man's first match with Firepower in #230, as Jack Taggert's been training extensively on a simulator, and the real suit's capabilities totally overwhelm Iron Man.
Eric O'Grady, the Irredeemable Ant-Man, was pretty much completely winging it throughout the entire twelve issue run of his series; he was constantly learning how to access his various abilities (like communing with and controlling insects or flying with his suit's extra jet legs). In fact, he scarred his immediate superior's face while trying to escape after stealing the suit to begin with. Later, after he became a cadet at Camp Hammond in Avengers: The Initiative, he discovers he can grow in size, too (with the possible limitation of this only happening in response to a threat posed by someone else turning giant with Pym Particles).
In Marvel's Young Avengers, teenage spellcaster Asgardian (later Wiccan) is shown to have difficulty using his powers. His boyfriend, Hulkling, helps him learn to control them with ordinary self-help books.
Way back in the origins of the New Mutants, Cannonball was only able to shoot himself straight ahead, and stopped mainly by running into things. It took a while for him to control his flight, much less realize he could steer himself and get any good at it. Luckily for him, he's physically invulnerable while "blasting" (and possibly immortal, depending on which retcon they're on at the moment), so he could always walk away from a crash. This was also the case with Nova to some extent, in the early issues of his first series; he could fly at supersonic speeds, but sometimes couldn't turn or stop in time to keep from crashing into things, particularly during a fight. Writer/creator Marv Wolfman also mentioned more than once (through other characters) that Nova had powers that he was completely unaware of; later series would eventually reveal these.
Parodied in the Great Lakes Avengers, with the Grasshopper. After spending a couple of pages setting him up as an important character, revealing his identity, origin, and mandatory superhero romantic troubles, he decides to exit the scene by engaging the "Maximum Jump" capability of his super-suit. It launches him into space and he dies.
The second Blue Beetle, Ted Kord, inherited the magical (or, as it much later transpires, alien tech) scarab that powered his predecessor's superhuman abilities — but couldn't figure out how to make it work for him. He never did — which didn't stop him from having a long heroic career as the Beetle under his own steam.
The third Beetle (Jaime Reyes), incidentally, gets along with the scarab like a house on fire. It just didn't take to Ted. It's implied by the scarab that the reason it didn't work for him is because he hung around Booster Gold too much, supposedly because of being exposed to too much of his "multiverse energy".
In the Silver AgeSuperboy stories, Ma and Pa Kent were shown helping Superboy hone his powers. Particularly true with flight. Unlike in Smallville, he figured out the thrust mechanism early on but had trouble with steering. In the Modern Age New Krypton storyline, Superman was shown to be an elite soldier because of his extensive experience using his powers, leading to him training fellow soldiers in the New Krypton military. Supergirl, by contrast, was able to activate all her powers but struggled with holding back.
In Sonic the Hedgehog, Mina Mongoose first using Super Speed usually lead to her slamming into things, ultimately leading to her confronting Sonic and begging him to help practice it. She also used it to get closer to him, as she had a crush on him.
Powers does this a lot, starting in the very first issue where a powers specialist police pathologist rants at length about the fact he has no idea how to do his job and has to retrain himself every day because every single powers operates on his or her own uniquely altered biology and there's no frame of reference for anything that they do. At least one hero meets an early end to his career when he kills a bystander while trying to figure out how to fly.
The heroine of Ghost took some time to learn to manage her intangibility: how not to walk through her garments; how not to drift while sleeping and wake up deep underground.
In the first couple of issues of Ms. Marvel (2014) the titular heroine has this problem with her Shapeshifting abilities. They start off tied to her emotional state (shrinking when she feels small, turning into Carol Danvers when she thinks of Captain Marvel) and she's unable to control them willingly at first.
Kamala: I wonder if I can do it again, this time on purpose. TRANSFORM!!!!
Superboy had this problem after he first appeared during The Death of Superman saga - he had flight, limited invulnerability (fire actually harmed him) and super strength and a strange ability to blow metallic things up. The last one he had no idea how it worked and it seemingly came when he was in a panic. After learning he had Tactile Telekinesis (which allowed him to mimic Superman's abilities to a point), he started focusing more and using it a lot better. Then came the rest of his Kryptonian powers, like his heat vision, which first manifested in accidentally singing Superman's cape (he wasn't happy about that.)
When she first showed up, Xadhoom had no problems at using her godlike powers, but she once mentioned it took a while to actually learn how to use them. She also didn't learn she has minor shape-shifting abilities until she pulled it by accident, and continues learning some new use of her powers until her Heroic Sacrifice.
Parodied in a Calvin and Hobbes strip where Calvin is standing around trying to get his butt to light up like a firefly, and attributes his lack of success to "not even knowing what muscle to flex".
Harry Potter and the Methods of Rationality: Harry spends several chapters conducting scientific experiments to figure out how Hogwarts works. In fact, he concocts a big series of experiments to have Hermione perform... And then quickly has to scrap the lot once the first one shows his fundamental assumption was completely wrong.
When, in Shinji And Warhammer 40 K, Shinji develops ungodly powerful psychic abilties to thwart Sahaquiel it not only completely destroys his ability to pilot Principio Eternus but makes him highly dangerous to everyone and everything. He then spends a chapter or (in a story where the chapters are long enough to be entire seperate stories themselves) being taught to limit them to a more manageable level by some monks. As proof that Tropes Are Tools, this arc is often criticised for being a classic Wacky Wayside Tribe.
In With Strings Attached, all the four struggle with their magic when they first get it, especially Paul, and they undergo a continual learning process throughout the book.
In Perfection Is Overrated, Bachiko has the power to rewrite people's personalities by stinging them with summoned bees. This proves more complex than it seems because 1)It's entirely possible for the rewrite to be too vague or too specific to fulfill the assigned purpose, 2)Removing one personality trait in order to influence a target's behavior in some way may not work if the target is acting this way because of other personality traits and 3)Unbeknownst to the user, a second sting, in addition to applying its own changes, completely undoes all the changes associated with the first. As a result, Bachiko tends to make overly dramatic and unsubtle changes to personality, such as making Nao extremely polite in an attempt to get her and Natsuki together, which tend to undermine her overall goals.
Notably averted in Ultimate Spider-Woman: Change With The Light. When Mary Jane Watson suddenly finds herself developing bizarre superhuman powers, it doesn't take her long to figure out how to use them. She's already an experienced fighter due to being a blackbelt martial artist, which makes it easier for her to determine how to best use them in a fight.
Kyoshi Rising; the title character is an Earthbender, but at the beginning of the story she is only a child and has no formal training whatsoever. She tries to teach herself Earthbending based off what others have told her (mainly stomping around and flailing her arms ala The Last Airbender), but can never move more than a few small rocks at a time (unless she gets angry). Once she gets some formal training, she progresses quickly.
A plot point in the Triptych Continuum is that alicorns have the powers of all three pony tribes, but haven't necessarily studied the mechanics of those abilities and don't come into their new state with automatic knowledge of how to make them work. This means Twilight is incapable of flight, while she appears to have Power Incontinence to a lethal degree.
Tony goes through a few iterations of flight testing with repulsor thrusters. His first attempt was just boots (and at 10% capacity) which gave him a faceplant... on the ceiling. Second test he got smart and added flight stabilizers on his hands (and only at 1% and then 2.5%), but still had some trouble before gaining control. His full flight-ready Mark 2 suit also took some time getting used to before he had flight control. He doesn't even intentionally create his iconic hand beams; he just accidentally finds out that having his hand stabilizers go off at full power while not in flight fires a blast of energy.
Ironically subverted by Obadiah Stane, the film's villain, who is able to match Iron Man blow for blow when he gets his own suit of armor, despite having never been shown to have any training of his own. However, he relies heavily on a targeting computer; when Iron Man disables that, he quickly proves unable to hit him with missiles from about ten feet away. Nor does Stane know about the dangers of his armor freezing up if he flies too high, a problem Iron Man had already dealt with earlier in the film and that he now exploits when Stane makes the same mistake he did. His proficiency is somewhat justified in that the Iron Monger suit was designed as a mass produced weapon that Stane could later sell to the military; it's implied that it's designed to be very easy to use as opposed to the specifically calibrated Iron Man suit Stark has.
Stark didn't have much trouble operating his original "escape" suit either, despite not having much — or any — practice with it (but he designed and programmed it, so he knew how it was supposed to respond). Since Stane's suit is just a bigger and beefier copy of Stark's original plans, presumably there was something about the original design that made it fairly idiot-proof. That said, the entirety of the Mk. 1 suit's armaments were a flamethrower, a manually-fired missile, fists and a manual start rocket boost. The flamethrower requires next-to-no aiming capacity and the missile missed... thank goodness for Splash Damage. Meanwhile Stark couldn't stop himself from constantly adding upgrades and modifications that certainly would have made his own suit more complex and fiddly. (Not to mention Perpetual Beta.)
Hilariously played straight in Iron Man 2 where the various corporations and countries (including North Korea) tries to replicate the Iron Man suit, only to be met with disaster each time. Justin Hammer's own demonstration even shows that, without proper knowledge, simply turning to the left can potentially snap your spine in two due to the hydraulics turning the torso too far. Subverted with Rhodey though, who not only managed to steal one of Tony's suits, but thoroughly beat Tony into the ground with it. Granted Tony was piss drunk, but that's still rather impressive. It's implied that Rhodey only ever saw the suit, but never actually wore it before then.
In Iron Man 3, Tony puts Pepper Potts in the Iron Man suit to protect her from flying debris. She tries to fight their attackers, but can't figure out how to work the suit, so Tony remotely takes the suit back when she is at a safe distance. Savin steals the Iron Patriot suit and has no trouble operating it. Also, it is revealed that the so-called terrorist bombings were really people who took Extremis and blew themselves up because they couldn't regulate their powers. When Pepper is injected with Extremis, she manages to control her powers and defeat the Big Bad with them.
X-Men: First Class shows more of this. Professor X hypothesises that Banshee's sonic scream should enable him to fly, so he encourages him to jump out of a second story window. Three guesses what happens.
Basically the main plot of The Meteor Man, where much of the movie is spent on Jefferson Reed learning to use his new powers, including flight (despite being afraid of heights).
A similar thing happens to the title character in Sgt Kabukiman NYPD: The first time his powers manifest, he accidentally cartwheels into a light pole; later, he tries to become Kabukiman, but somehow turns into a clown; even later, he learns he can fly, but due to not being used to it, he throws up, and it lands on an asshole lawyer below him.
Batman Begins shows Bruce Wayne experimenting with the technology that would eventually become part of his iconic identity, learning from his mistakes (bouncing off that fire escape had to hurt!) and upgrading accordingly.
Chronicle features a lot of this when the three teenagers discover their telekinesis, starting off with fairly basic experiments with redirecting thrown baseballs and assembling lego sets (Matt having great difficulty getting the bricks to stay together), to testing forcefields by stabbing each other in the hands with forks. Even after they think they've managed to master their powers, more of this trope crops up when Steve learns how to fly; while Andrew gets the hang of it very quickly, Matt's first three attempts result in him crashing to the ground.
Captain America: The First Avenger: After Steve comes out of the tank with super-strength and speed, he spends the next minute or so running into store fronts and cars while trying to turn. Also apologizing. A lot.
In Man of Steel, it took Clark a few tries to figure out how to fly. Clark and the Kryptonians had to master Super Senses. Fortunately for Clark, he learns to shot web before the other Kryptonians do which gives him an edge in the fight until it's down to Zod who finally figures out the remainder of his powers.
Covenant in the Chronicles of Thomas Covenant spends a remarkable number of pages not having a real hang of his own Wild Magic. Most of it is pure instinct, even without his knowledge early on. It's not until the second trilogy that we see him directing it toward definite purposes, complete with a training regimen... he uses his wild magic to shave, precisely to teach himself control over it.
Say what you will about the Doorstopper length of Robert Jordan's The Wheel of Time series, but it does allow the channeling characters a realistic period of time to get a grasp on controlling and developing their powers. Notably, none of the characters become Instant Experts, but have a learning curve of three or four books before they gain consistent control. Nyneave takes a full seven books to overcome her block. Learning to use saidin without a teacher is so difficult that Rand finally has to trap a Forsaken to keep from getting himself killed. Later, Nynaeve and Elayne hold another one hostage in order to learn lost techniques that have stayed lost for a good three millennia.
Dragaera: Vladimir Taltos has no freaking clue what he's doing with his new Empathic Weapon, Godslayer and has gotten himself in a lot of trouble with such screw-ups as accidentally destroying a sorceress's soul in the process of blocking something nasty she threw at him.
Richard from never learns how to use the vast majority of his abilities... except, of course, the ones that are absolutely necessary to allow him to save the day. Richard's magic appears to be keyed to strong emotion; a big deal was made of whether or not he could actually use his anger in the first book, as opposed to simply keeping it locked inside himself.
Subverted in the case of swordplay — which is, let's face it, the first thing to master when trying to use any magic sword's first and foremost super power. Getting magic swords that can cut anything is great — for knights and swordmasters. For anyone else, it's a health risk. Richard's a woodsman, the most experience he'd have with blades would be limited to a machette and a skinning knife. He'd have to learn swordplay like any other, right? No. The Sword of Truthcan share the collective combat experience of all previous users with the Seeker; Richard of course learns this while, and promptly uses it during, a fight with 30 — that's thirty — Baka Ban Mana blademasters. They're guys who spend most of their lives training swordplay, each day, all day, dawn till dusk. Right. He actually lampshades it right before that fight, thinking that against one man he is virtually unstoppable — but only because the sword cannot be parried, and so he can count on getting one strike through.
There is a villainous case in book 4, where Jagang takes over the mind of a wizard. He can use simple telekinesis and throw fireballs, but never uses more advanced powers like Deflector Shields or tranfiguration.
Matilda spends a substantial amount of time trying to figure out the ins and outs of her "push-stuff-around-with-her-eyes" (telekinesis) power.
In the Codex Alera series, we see the Academy is where most Alerans go through this learning process. However, when Tavi becomes aware of furies, the person goes through a Training from Hell for months, which we see briefly in the second to last book.
The better part of a chapter of Life The Universe and Everything is devoted to Arthur Dent learning to fly. By accident. To put it simply, he was falling, and got so distracted that he missed the ground. He does eventually become adept enough to teach another person to fly, and they end up having sex in midair.
In each of the Incarnations of Immortality books, the protagonists have to get the hang of being the Incarnations of Death, Time, Fate, War, Nature, Evil, Good, and Night, respectively.
In Mistborn, it turns out that phenomenal cosmic power does not include the ability to think its effects through. An Evil Counterpart is also present and capable of countering it with opposite-but-equal force, so all attempts at figuring out the power either fizz out or 'splode. Rub out the perpetual clouds of smoke, see the sun for the first time — no block. The sun looks a lot bigger than it is supposed to. The day face of the planet catches fire. Spin the planet to save that face — no block. Try to stop the tsunamis that result — block. Also, gloating.
Not knowing how to properly control magic in the Inheritance Cycle will likely kill you from either a rebound of magical energy or, more likely, draining your life force away before you can cancel the spell. It's also been said repeatedly in-universe that truly mastering the art of magic takes decades of practice and diligence. For the first book and a half, Eragon's progress follows this trend, as he slowly progresses from struggling to lift a rock with his mind to effortlessly casting fire-based spells. Of course, then he undergoes a crash course in magic with the elves and then becomes half-elf during the Blood-Oath Ceremony, completely eliminating the need for a slow progression.
He's still learning clear through to the last book, but after the Blood-Oath Ceremony, it's less about how to use magic, and more about learning what he can accomplish with it.
Most of the mutants in Gone suffer from this, particularly Sam. Strangely, Caine and Diana have already figured out how to use their powers because Evil Is Cool and Good Is Dumb. Diana and Caine spent a while practicing their powers before coming down to Perdido Beach. It was said in the first book they'd had their powers for a couple months.
Shonsu in The Seventh Sword trilogy, by Dave Duncan, spends all three books learning to use the abilities given to him by a goddess. When he is first granted the abilities and knowledge to be the world's greatest swordsman, he has no idea. As the story progresses, he learns more and more about his capabilities, usually as the situations arise. This even applies to textbook-type knowledge, which actually works really well in the story.
In Just Another Judgement Day, there's a humorous scene at the Adventurer's Club when a wannabe supervillain with no clue how his (stolen) magic rings work accidentally teleports himself into the midst of a huge crowd of Nightside heroes, rather than into the neighboring club he'd intended to rob.
Harry Potter builds this trope right into the setting. You've got magical powers? Great! You still have to go to school for seven years to learn how to use them. Both young Harry and Tom Riddle are able to occasionally "will" something to happen, but the effects are haphazard without training.
All young witches and wizards can use magic during times of stress or when feeling extreme emotions, though the effects are notoriously unpredictable (though they'll often reflect the emotion the kid's feeling; when Harry wanted to escape Dudley and his friends, he apparated on top of the school chimney, for instance). It's shown that they can gain some control over it on their own, like Lily did as a kid, but to do anything functional and avoid losing control of their powers they need schooling.
Deliberately invoked in The Immortals when Emperor Ozorne turns himself into a Stormwing to avoid punishment. As the Stormwing queen Barzha tells him, he just lost all his mortal magic in exchange for immortal magic, which he has no idea how to control. Sadly, he gets a grip on it pretty fast.
In Galaxy of Fear, young Tash Arranda is an untrained Force-Sensitive. The Force is a fantastic power... but she really doesn't know anything about using it beyond what a sympathetic Luke Skywalker told her in the first book: that she should trust her feelings. When she fails at Jedi anything in The Nightmare Machine, her memory of this failure sabotages her repeatedly in Ghost of the Jedi.
For a while, I thought I might be — or could be — a Jedi. But now I think that was just a fluke. When we were on Hologram Fun World, I didn't know what was happening even though we were in danger. Now I just feel like I'm going crazy. That's the opposite of what a Jedi is.
In Animorphs, the kids got the general hang of morphing easily, but had to watch every new morph because they risked losing control of it. And in some cases, like termites, they never morphed them again.
Legacy of the Aldenata: The Posleen inherited all of their technology from their Neglectful Precursors, and they have no idea how most of it works. This can lead to some humorous bits, such as when a computer helpfully informs one Posleen about incoming artillery fire and he just stares at it like a moron.
Peter Petrelli , both in season one (where he learned how to control his empathic powers from Claude) and in season two (where he got amnesia and forgot both which powers he had and how to use them). This seems to be one of the recurring problems which always almost brings about an apocalypse of some sort. Hell, in the beginning of Season One Peter didn't even know what his power was, having spent his life around five people with a power he could copy.
Arthur Petrelli doesn't seem to have this problem. He has a pretty good handle on how to use the powers he stole from Peter despite not having seen him use them.
There is also serial killer Sylar, who can use powers better than the person he stole from due to his power of "Intuitive Aptitude" which is the ability to analyse how things work, including brains (which is where powers manifest). However, Sylar seems to need a fair bit of training when he learns to take powers without examining the brain. Of course, we're still not sure how this works.
This is the entire premise of the show The Greatest American Hero. The hero lost the manual in the first episode. It's worth noting that Ralph finally got a replacement super-suit instruction manual in one episode. He loses it when, experimenting with shrinking powers, he gets startled by an ant and returns to normal size... leaving the manual microscopic.
Used in Smallville a number of times as Clark's emerging powers make themselves known, most notably with his heat vision and X-ray vision. Clark spends all the way up to Season 10 unable to figure out how to fly, while Kara and other Kryptonians can do it in a few minutes. Clark ends up accidentally firing off his Eye Beams (the first time he realizes he has them) by watching a sex ed video with a new hot teacher (Krista Allen). It's not difficult to see what the writers were trying to get across, especially since he triggers his second time by thinking of his crush Lana. By the end of the episode, he can trigger the beams on demand (such as by incinerating a bullet in flight).
Also, Kamen Rider V3 has to figure out all of his abilities due to Riders 1 and 2 being killed before they can teach them to him. (They get better.)
Kamen Rider Super-1's powers were meant to be controlled remotely. When the base (and machines) went kablooey, he had no idea how to activate his transformation, and it took six months of study at the Shaolin Temple to be able to Zen up his transformation (it... uh, makes more sense in context).
Kamen Rider Kuuga has to learn how to use the abilities of each form, usually with help from his friends. He also tends not to have a new form until it reveals itself to him. The Arcle actually does come with a manual, but it's translated only a very small amount at a time, and the Grongi ain't gonna wait for Yuusuke to figure out how the shiny suit works.
Kamen Rider Faiz was not meant to have the armor but is one of few who can use it. There are a lot of features Takumi doesn't know about until he stumbles onto them. In one episode, Delta summons a rocket bike. Takumi summons the one he never knew he had by entering the same code. It gets destroyed in the same episode as he's not as good with it as his opponent is with his own. Of course, he still has a Cool Bike.Why Takumi is one of the few who can use it is something else nobody knows at first, and is a doozy when revealed.
Kamen Rider Fourze literally struggles to transform and use his switch-weapons in the first episode. Yuki has to explain the transformation sequence to him, and Kengo communicates with Fourze mid-fight through his radar's built-in communicator in order to explain what gadget does what. Without all that help, Gentaro would've been flying around randomly and firing missiles everywhere without even touching the very first Monster of the Week once.
There was a scene in the first episode of Power Rangers Ninja Storm where the Rangers try to figure out how to activate their morphers. And then when they actually go out to face the bad guys, they struggle for a minute to remember the By the Power of Grayskull! phrase.
In Power Rangers Turbo, forming the new Megazord was difficult, and the Zords banged into each other a few times before someone got out the manual. What makes this one interesting is that, in The Movie, they could pull it off by being stationary. They just couldn't do it at high speeds.
In a relatively unremarkable body switch episode of Farscape, Rygel (the tiny frog-like Napoleon) is occupying John Crichton's body when he finds himself needing to urinate. John leads him through the steps, but when it comes to zipping up... well, it didn't go well. Let's not forget that John was in Aeryn's body while giving the instructions, for added hilarity. Aeryn later hints that she did certain things in John's body as well.
British superhero drama Misfits really goes to town with this trope. Of the five protagonists, only Simon (whose power is Invisibility) can exert any kind of deliberate control over his power, while the others remain baffled and exasperated by their ungovernable abilities. Both Kelly, who hates being telepathic and wishes she could just turn it off, and Alisha, whose "power" of pheromone manipulation — which causes anyone who touches her skin to experience such violent surges of lust that they will generally attempt to rape her — can do nothing to mitigate or restrain the effects of their powers. Curtis finds his power of time manipulation to be infuriatingly sporadic, and then there's Nathan, whose power of Healing (and effective Immortality), works so incredibly slowly that it's possible for him to die, and only come back to life several days later — to find himself buried alive, naturally. It is, however, a little early in the Series to deem them all trulypower incontinent.
The Objects from The Lost Room have shades of this, when someone even knows what they do or how to activate them. This is doubly true for the abilities of Object combinations, which don't always have anything to do with combining the abilities of the individual Objects.
The pilot of The Invisible Man involved Darian being implanted with a gland that can turn him invisible, after which he has to be taught how to activate it, and then he experiments with it and learns to do things the scientists who developed the gland didn't even think were possible. The first time they get him to go invisible is by releazing tarantulas in a locked room with him. Considering Darien has arachnophobia (and his brother would know), this is a good way to trigger a massive generation of adrenalin necessary to activate the gland. When Darien tries to spy on a nurse and a soldier getting in on, his excitement causes his adrenalin levels to drop... and he gets a black eye from the pissed off soldier. Learning yoga helps control it. In another episode, Kevin Fawkes's RNA is injected into the gland in order to "revive" Kevin's ghost in Darien's body. Naturally, Kevin has to relearn how to use the gland.
The members of No Ordinary Family have to spend quite some time learning the strengths and limitations of their new abilities. It occasionally goes poorly.
The pilot of The Flash has Barry learn about his ability and limitations. The first time he accidentally activates it, he tries to catch a bus... and ends up miles away on a beach. He has a hard time stopping. The only thing that helps is running on water, which absorbs a lot of his momentum. He also faints frequently due to his metabolism going into overdrive, turning him into a Big Eater.
The 2014 remake has Barry try to run after discovering his power, only to accidentally end up in a van that happens to be full of clothes to soften the impact.
Vampires in the Forever Knight verse have to learn to control their powers right after being turned, especially the trick of not being overpowered by the hunger. That's why most of them have masters guiding them for a while.
On Teen Wolf, werewolves do not have instinctive knowledge of how to control their powers, or even knowledge of all the potential powers that they might have. For example, Peter Hale has exhibited various telepathic powers as both an Alpha and a Beta that Derek and other Alphas do not seem to know how to use.
One Mutant X episode has a young boy kidnapped for ransom. It turns out that the boy is an Elemental New Mutant capable of throwing fireballs. However, his is young, so he's not sure how to control his ability. The first time it manifests is during the kidnapping, when he accidentally burns a hole in a kidnapper's hand. At the end of the episode, he finally learns to produce fireballs on demand by copying Brennan's Pstandard Psychic Pstance when he's charging his electric powers.
There's also a bit of this when the team receives an upgrade. Brennan learns he can create a continuous blast akin to an ion engine with his hands, enabling brief flight. Shalimar becomes even stronger and can hear someone sneaking up on her while working out with loud music in her earbuds. Emma's Psychic Powers are boosted Up to Eleven. Jesse learns to make other things intangible.
The roleplaying game Scion has the character channeling their divine power through Birthrights — gifts from their god-parents. If someone were to steal a Birthright, they could use all the real owner's powers that it channels — but the chance of failure, and the penalties, are significant though, meaning most characters who try this end up dying to this trope.
The Sorcerer class in Dungeons & Dragons is based on innate spellcasting power. First level sorcerers can create light or perhaps burn something with a bit of acid, but get more powerful with time. However, they are greatly limited in the variety of spells they can cast, as they have to figure them out themselves instead of learning them from scrolls or books.
Brought up infrequently in LEGO's BIONICLE franchise. The Toa Metru spend almost a year's worth of story not knowing how to activate their mask powers — they eventually discover them in the movie Legends of Metru Nui. Forming Toa Kaita fusions is another power of theirs they didn't know how to master. Universally, the much more powerful Toa Nui fusion is something that no Toa ever managed to achieve, and is as such seen as a mere fable. And in the canceled 5th movie, Kiina and Ackar would have struggled to keep their newly acquired Elemental Powers in check.
The Pokémon Ditto has only one power — Being able to copy those that belong to its opponent. (It's also immune to being paralyzed, but that's beside the point.) However, Ditto cannot copy the opponent's HP and all the moves it copies come with only 5 PP, showing its inability to master techniques on the spot.
Rumia can generate a field of darkness to protect herself from light, which hurts her, but she can't see through her own field of darkness; she can often be seen bumping into trees midflight. Apparently, ZUN thought it would be funny to make a character's powerful-sounding ability (control of darkness) actually be useless.
Keine can hide and "eat" history, as well as create entirely new history in her hakutaku form, which would make her one of the most powerful characters in a setting already overflowing with Story Breaker Powers if she had any idea how to use it. The only time she even attempted, hiding the Human Village during the Imperishable Night, the player characters found it easily anyway.
The backstory to the NESTS saga character Nameless in The King of Fighters reveals that he had a number of problems controlling his pyrokinetic abilities. Most of his time after testing was spent in the infirmary recovering from severe burns, and on his first real assignment he killed somebody just by tapping them on the shoulder.
Much of Final Fantasy VI focuses on Terra's inability to control her powers as a half-Esper.
Final Fantasy VII. After his defeat at Nibelheim, Sephiroth is inactive for 7 years, trapped in Mako until he returns with Jenova's powers. There's some debate on whether that comes down to Sephiroth learning how to control Jenova or the other way around, but Word of God has said that Jenova was not in control. Although that Word of God was released 10 years after the original game.
In Dot Hack games, both Kite and Haseo needs to learn how to use their powers. Kite got off lightly, since his Twilight Bracelet can be used easily (with the catch that if he has too much viral infection, he'd, quite simply, die). No mishaps there (except player-induced). Haseo however, basically had to undergo a lot of training to obtain his Epitaph Power as Skeith. The first time he got it out, he nearly comatosed a group of people. Afterwards, he's inclined to pull this off to anyone that threatens him, comatose or no. Inevitably, he loses control of Skeith since he used it with such a reckless abandon. Were it not for Kuhn's special power, he would've permanently comatosed someone.
In Shadow of the Colossus, although he's a crack shot with his bow, Wander doesn't know much about how to use his sword except that it shines when he is getting near a colossus and "point stabby end at colossus; stab." The eventual backstory revelations imply that he stole the thing, which would explain why he's so awkward with it.
"...Please, a moment. My body is not... cooperating."
The constant bane of MMORPG veterans is newbies who get levelled up too fast thanks to Min-Maxing friends, and end up being very high level with absolutely no idea how to use any of their equipment or abilities, or the basic features of the game. Even worse are those who simply buy high level characters, literally hitting the level cap without ever having fought an enemy.
City of Heroes players suffer from this trope particularly due to the sidekick system. A low level hero can be temporarily promoted to a high level so they can join a high level instance, but they do not gain any new powers, nor does it miraculously turn a new, low-level player into an experienced veteran.
World of Warcraft also has this apply to the ability to pay to change your talents, or buy an alternate set of talents. As such, players may be quite good at using their current talent tree, but may need some adjustment while switching to others, as a Warrior might be quite good at the DPS Arms tree, but not as good with Fury (which is also DPS), let alone tanking with Protection without quite a bit of practice.
Another cause of this syndrome is a "Foundry" or similar system that lets players create their own content. Some will create easy "farming" missions that grant plenty of experience points with little "experience".
In Breath of Fire III, Ryu is born as a baby dragon, and his first few shapeshifts between human and dragon forms (which occur outside of actual combat) are completely uncontrolled. Although the player gains the ability to transform at will during battle, it is not until later, when he reaches adulthood, that he has full control over his transformations.
Played with in Super Metroid and Metroid Fusion. Samus always had the ability to walljump and shinespark, but learns to use it from the Zebes animals. When the SA-X appears, it is completely unable to do such techniques, and neither uses the rest of its abilities at their fullest potential.
However it is implied that the SA-X would know how to use the abilities as it's explicitly stated the X take knowledge from the host (so it would know by virtue of having infected Samus once). It simply doesn't use them because it doesn't see any need to do so as can be evidenced by its preference in using brute force.
Bang Shishigami from BlazBlue was only told two things by Platinum; that he had a Nox Nyctores, which are insanely powerful, and that its ability could very well save several people. She didn't bother telling him though what it was and not even how to activate it.
Fairly well done in Second Sight, where John escapes a hospital with Laser-Guided Amnesia. He has a lot of psychic powers but doesn't know about them, until they manifest themselves by an appropriate challenge. For example, he finds himself tied to a cot and unable to get free. Suddenly, he realizes he can will the bonds to open and the door to unlock. He's also weak and hurt. He clutches his head... and suddenly feels better via psychic healing. A guard tries to stop him and threatens him with a gun. Once again, John gets a headache and fires a sphere of psychic energy at the guard that sends him flying across the room, breaking the guy's neck. This all culminates at the end when John realizes that most of the events of the game are the manifestation of his Precognition ability; i.e. the game events are a possible future.
Kingdom Hearts 3D: Dream Drop Distance: Toward the end of the game Lea receives training to use a Keyblade, then pulls a Big Damn Heroes in the climax to save Sora... with his Eternal Flames. After Sora is woken up, Lea reveals that he couldn't get his Keyblade to materialize.
Shirou not only doesn't know how to shot web, he doesn't even know it's web he's supposed to be shotting!! Ahem. At first, he thinks he's supposed to be using strengthening magic, which he sucks at. Eventually, he figures out that he is much better at projection (magic that involves creating temporary replicas of real objects) and, although it's immensely taxing, picks up on that and becomes very good at it. During Unlimited Blade Works Archer reveals to Shirou that it's not projection he's good at, it's visualizing the exact nature of an object and creating it from his mind alone, which Archer eventually developed into a Reality Marble that turns him into a pure badass. At the end of that route, this allows Shirou to tap directly into his full potential. In Heaven's Feel, Shirou gains a more instinctual knowledge of his true powers through a Dangerous Forbidden Technique and being coached by Ilya, but the aforementioned technique causes brain damage and eventually kills him because that's the "From Bad to Worse" route. (Though he recovers somehow in the True End.) Oh, and in all cases Shirou still has a hard time projecting things accurately, which means they break easily.
This also happens with Sakura, who never received proper training as a magus and because of this has trouble controlling her magic. She does wind up being able to use it by instinct... when she goes crazy and gets access to Angra Mainyu's gamebreaking powers. Oh, Crap, indeed.
After the title character of Spinnerette acquires spider powers from a gene-splicing ray, she gets to literally figure out how to shot web. Like movie-verse Spidey, she eventually learns how to do it; unlike movie-verse Spidey, though, it doesn't come from her wrists... Sahira, a biology major, almost dies laughing at this:
The full capabilities of the Monster in the Darkness from The Order of the Stick have never been revealed. The in-comic reason is speculated to be that he's too... childlike to know his full potential. Xykon implies once or twice that he actually knows the exact limitations and capabilities of the Monster in the Darkness, even if the Monster doesn't; he's repeatedly stated that the Monster is his trump card, and he has no intentions of bringing it out until its planned debut, or until things go completely out the window, whichever comes first.
The girls instinctively learn how to command their powers in M9 girls!. Later on, they train to fine tune them.
Even though she gained her alternate form some time ago, Mye from Charby the Vampirate doesn't know most of the forms abilities. While she did suddenly learn she could teleport during a fight, and apparently has much greater strength, she still hasn't gotten around to learning to fly and mentions the fact to herself every time she gets stuck in a situation where flight would get her to safety.
In Sparkling Generation Valkyrie Yuuki, the main character Yuuki is selected to be the next Valkyrie, and is flung into several fights with no idea how to use her new powers. She's forced to more or less play it by ear early on. That's not the least of her problems, though...
Agatha goes through a period of this early in Girl Genius, but for "sparks," this is normal. In fact, she would have finished going through the Shot Web phase years ago if she hadn't had a Power Limiter locket put on her for her own protection. Following the locket's removal, Gil remarks that she didn't break through so much as ease through.
Rose hasn't put too much effort into figuring out her Seer of Light powers yet, preferring to hone her magical abilities. Jade isn't even sure what being Witch of Space means, beyond apparently having "breeding duties" involving frogs and something about stoking a forge.
This trope is mostly averted when each of the kids reach God Tier. John, Rose, and Aradia all display instant mastery. On the other hand, Jade, who inherited both God Tier and First Guardian powers is still working her way through the latter abilities.
Happens frequently in Kagerou, one of the more notable examples being Kano learning how to use the magic sword he's given. He still hasn't quite gotten then hang of it despite ongoing training and having had to use it a few times to avoid being killed.
Kano: Um, Cho, how am I supposed to hold it? It seems to have a number of... teeth.
A more straightforward example comes when Tedd suspects he finally has a power of his own. Grace encourages him to try, but after a pause, he simply asks, "How do people cast spells?"
League of Super Redundant Heroes features Lazer Pony, who discovered that he can shoot lazer beams from his eyes, but doing so permanently blinds him the first time he does it. Having a sight-based power while blind is extremely impractical, but LP has been seen trying to learn to better use his powers, particularly with the help of someone "aiming" him.
In one episode of Full Frontal Nerdity, Frank runs a superhero campaign in which, reasoning that "Superman was always Superman", he lets his players start with ludicrously overpowered supers... who don't really know how to control their powers. Multiple destroyed cities ensue.
In the Kings War arc of Roommates the injured Monster Roommate Jareth gives all his power (and kingdom, and resposibilities, etc.) to his best friend (and Token Good Teammate) James with literally no explanation; cue this trope ensuing on a grand scale and at the worst time.
In Little Robot Big Scary World, BIP has to learn his functions through experience, as his creator died before he could tell him how to use them.
How the first few chapters of morphE play out. The five seedlings have awakened as mages and have to learn to use their magical abilities. Their teacher, Amical, throws them into lessons which become increasingly difficult to rush their learning curve.
In Chirault Bethan becomes intangible. It seems to give her a lot of sweet options, from going through objects and flying to dispelling magic by touch. However, she still has a problem with not falling through the ground: the gravity does not affect her, but she thinks that it should...
Odin: Your whole FACE is orange! C-can’t you see it!?
Ava: I CAN’T SEE MY OWN FACE!!
A common problem in the Whateley Universe. Fey couldn't do magic at first, and kept accidentally firing off hobgoblins — the psychedelic squirrel hobgoblins wrecked her whole school. Phase at first couldn't keep from changing density, couldn't control his strength when he was extra-dense, and couldn't keep from sinking into the floor when he was intangible. At first, Generator could only cast a single PK charge into an inanimate object for a short while. They've all gotten much better at it.
In fact, one of the things that makes the character Mimeo so scary is that he's not just a powerful Mimic who can copy multiple superpowered opponents' power sets at once, but he's also got years of experience under his belt (he's a Whateley alumnus himself, among other things, so he did have formal power training) and so can usually avert this trope because whatever powers he's copied from you, they're probably similar enough to ones he's had before that he can skip the "figure it out" step and just use them competently straight away.
Several campaigns in the Global Guardians PBEM Universe were built around the premise that the characters had literally just got their powers, and had no idea at all how to use them. For the most part, these campaigns resembled the first season of The Greatest American Hero. Occasionally, this was used to justify an experienced hero learning to use a new power as well.
In Worm, while most parahumans have a learning curve for their power, this trope comes into play most when people with powers like Grue's or Regent's are trying to use someone else's.
Princess from The Powerpuff Girls acquires powers like the heroines' several times over the course of the series, by various means. She fails to beat them every time, but never learns a lesson about it.
The X-Men: Evolution animated series used this a lot in the first season introduction stories, most notably for for Kitty Pryde and Rogue, but it virtually disappeared after that. That's because they were being trained specifically to control their powers, and other characters (Cyclops, Jean, Nightcrawler) had been using their power for years but still had trouble getting it right from time to time.
In the very first episode the new Guardians have a powers practice that is the definition of how How Do I Shot Web?. None of their Elemental Powers are under control yet, flying is... iffy, even for the naturally inclined Hay Lin and when the girls try to Caleb from Cedric Will attempts to do an All Your Powers Combined attack and hits everything but Cedric. They do pull it together in the second episode and are seen practicing some more in later episodes.
Will:(after their first practice) ...I think we've destroyed enough of Heatherfield for today.
In the second season finale, Cedric falls victim to this trope after devouring the Big Bads of seasons one and two, consequently gaining their powers, as well as gaining the powers of all five heroines. Despite having by far the most raw power of any villain in the series, he is unable to utilize his new skills to anywhere near their full potential. This, combined with new transformations for all five heroines, led to Cedric's defeat in a little more than five minutes.
A recurring problem for Ben, especially prevalent when he gains a new alien form and has no idea what it does. The first time he turned into Cannonbolt, not only could he not figure out how rolling up into an armored ball was useful in combat, but he kept losing his balance and falling over backwards when he tried to stand. Reaches its ultimate conclusion in Ben 10: Alien Force with Alien X, which is seemingly omnipotent, but since Ben only gets to be one of its three personalities and the other two are constantly at odds with each other (the only thing they agree on is that they want Ben to provide tiebreaking votes for all their thousands of years worth of disagreements before they get to what he wants to do), it's nearly impossible to get it to do anything. (It just stands perfectly still, stiff as a board, completeley unresponsive to anything. Ben later learns that this is a serious problem, because he can't turn back until he can convince the other two entities to agree on it, effectively trapping him in the nonresponsive Alien X form.
Same applies to Ben's Evil Counterpart Kevin 11, who instead of utilizing the full array of his Omnitrix powers (i.e. phasing, super-intelligence, super-speed, machine control) pretty much prefers to just either smash stuff or blast stuff. In Ben 10: Ultimate Alien Ben has to point out to him that he can phase through objects. He does get more creative in his power usage after realizing he's got so many different abilities, though.
There's also the ever-constant problem of the Omnitrix not giving him the alien form that he desires. Acting like a puzzle of sorts akin to a tumbler lock, at first, Ben would quite often be transformed into an alien that he didn't want to be. He does get a little better over time, discovering new aliens altogether and their powers, but it still acts against him. Thanks to some guidance from the Omnitrix's creator (much to his constant frustration), Ben eventually does gain full control over the Omnitrix in Alien Force, even being able to transform at will by speaking the alien name or thinking it. He ends up saving the universe at the expense of overloading the Omnitrix, forcing him to relearn EVERYTHING he learned over the past few years about unlocking i's powers. Even in Omniverse, he has almost complete control over it, but it still likes to screw him over every once in a while. He pretty much lampshades it when he wanted to transform into an alien that excels in physical strength, and gets turned into a Galvan (a small, froglike alien known for its brains, not brawn.)
Sometimes I think this thing just plain hates me.
However, in Omniverse, it's Flanderized to the point that he almost never gets the alien he wanted. When he finally gets to confront the inventor over the supposedly upgraded version never working as intended, Azmuth tells him that he's just too rough on the controls (apparently, the way he dramatically slams his hand down on it to activate it before a battle is the culprit.)
Worse, each model has different ways of tormenting him:
In the original series, once transformed there was no switching aliens or changing back until the Hour of Power ended, and it would take quite some time for the Omnitrix to let him change again. Also, it sometimes gave him the wrong one.
In Alien Force, there's no mistransformations and he can change from alien to alien! The bad news is mistransformations are how new forms were unlocked - ten means ten now, PERIOD. In season three, he tampers with it to unlock more aliens (Vilgax is returning, after all.) and ends up making it play by original series rules, for better or worse (sometimes worse.) He can still change from alien to alien, though.
In Ultimate Alien, the Ultimatrix can make his aliens go One-Winged Angel... but there's still mistransformations, and it lacks some features the Omnitrix had, which he finds out about by trying to use them only to find out, no can do.
In Omniverse, the new Omnitrix has every alien he's ever had! Too bad no matter who he tries to select, what he actually gets is apparently completely random. So is the time limit; he's stayed in the same alien form for extended battles, or had the Omnitrix last only a handful of seconds and not let him change again.
In Project G.e.e.K.e.R., the eponymous character Geeker has almost limitless power as a genetically engineered cyborg. However, Becky stole Geeker before he could receive the programming which would allow him to control those powers (and allow the antagonist to control him). Thus, Geeker generally discovers his powers by accident, and has difficulty controlling them.
Danny in Danny Phantom constantly gets new ghost powers with some conjunctions to Puberty Superpower every so often and as per usual, half of them are often hard to control.
Duplication is a frequent issue for him and his Ghostly Wail started off as a Dangerous Forbidden Technique, among others. He eventually got most of it mastered by the end.
Danny:(creates shield) Awesome! How'd I do that?
Let's not forget that incident in Memory Blank after Sam recreated the accident and Danny was having trouble with a simple ecto-blast and it came out the wrong end. We did get a cheesy line out of Tucker:
Tucker: Be careful where you point that thing!.
Valerie played it straight and averted it. With her first suit, it took her a while to get the hang of it and it was pretty clear in her first few hunting ventures that she was new at the whole ghost-hunting thing. But, when she got the upgraded suit from Technus, she knew how to use all the equipment and what/where all her weapons were, despite most of it being drastically different.
A popular Fanon for that is that the vehicles are keyed into a specific virtual avatar (since they were created for individual characters) meaning Odd-in-Yumi and Yumi-in-Odd were stuck with the vehicles keyed to the bodies they were currently in. This doesn't explain why Aelita and other characters can piggyback on another's vehicle when needed (and William stealing Ulrich's Overbike in Code Lyoko: Evolution) but oh well.
One episode of The Batman centered around The Penguin obtaining The Green Lantern's power ring, and his efforts to figure out exactly how it worked. When he obtained The ring himself, The Batman also had to learn how to use its powers. Which he did almost immediately, just the ring started running out of power shorty after he got it. There's a reason for that.◊
Come to think of it, Darkwing ('Arachnoduck', Spider-Man-style stuff), Launchpad (Heavy Mental, psychic powers), and Gosalyn (Slime OK, You're OK, ooze-based abilities) don't fare any better when they get superpowers.
Also multiple instances of people randomly getting suited in the Gizmoduck outfit by accidentally saying the command code "Blathering Blatherskates." It doesn't help that the suit is also a unicycle. How many people that aren't wearing clown makeup can ride one? One apparently, and it took him some time to get used to it before he could actually protect Scrooge McDuck, Duckburg and St. Canard.
One episode has Raven and Starfire body switched and having to figure out how to use each others' powers. Starfire and Raven's learning experiences, interestingly, are about attitude rather than the powers themselves. They both have powers tied to their emotions, but while Starfire's only work when her emotions are allowed to flow free, Raven has to keep her emotions under strict control lest her powers go off unexpectedly and wreak havoc.
The entire storyline of the series is fundamentally about Aang mastering Water, Earth, and Fire bending to become a "fully-realized Avatar".
Katara also goes from not being able to consciously control a few liters of water to being a waterbending master.
Behind-the-scenes info for Combustion Man from state that he got his mechanical arm and foot after blowing them off while learning his ability to shoot explosions out of his forehead when he was younger.
In the Sequel Series, Korra has a big problem learning how to Airbend, even though the other three elements came naturally to her.
In the animated series of Legion of Super Heroes, Clark Kent is still figuring out how to use his powers in the first episode.
Superboy, being a clone of Superman, has some of the older hero's powers, but does not know how to use them. This sets up tension between the two as Superboy wants to learn from Superman and sees him as a father while Superman is (understandably) disturbed by Superboy's existence and wants nothing to do with him.
In season 2, Blue Beetle Jaime Reyes has powerful suit of Adaptive Armor capable of creating just about anything he can imagine and even has Universal Translator capabilities. Too bad he has no idea how to use any of the Scarab's powers at first, and the Scarab's Artificial Intelligence hurts more than it helps since it always suggests the most violent and destructive approach to solving any problem. In "Salvage" the Scarab doesn't inform Jaime that it can communicate with the monster that's kicking his and Superboy's behinds until Jaime rhetorically asks if it can do so because the Scarab sees peaceful communication as a sign of weakness.
The Reach abductees have just about as much trouble with their new powers as you'd expect. Even after a couple of months, Virgil has trouble levitating a trash can, and Tye can't even turn his power on until the end of the episode.
In Iron Man: Armored Adventures Tony's first controlled flight in his Iron Man armor has him ding a few buildings but manages to pull it together. Rhodey's first foray goes so badly he creates a crater in the ground when he crashes and swears never to get in an armor again; that same episode Happy Hogan finds the armor and manages to get the hang of it so fast that Tony can't stop gushing about how good he is with it.
Averted in an episode of Justice League Unlimited, "The Great Brain Robbery." After inadvertently swapping minds with the Flash, Lex Luthor seems to fare pretty well in his new body, and the other League members have a hell of a time trying to stop him.
When Scott Lang from The Avengers: Earth's Mightiest Heroes first tries to use Hank Pym's Ant-Man gear for a bank robbery, he finds out by chance that the helmet allows communication with insects. Also, when he tries to use Pym Discs to make the stacks of money pocket sized, he accidentally makes them shrink smaller than microscopic size instead.
In Ultimate Spider-Man, one episode has him switch minds with Wolverine. Wolverine has no problem with Spider-Man's agility, but doesn't try to use his other powers. When he tries using the Webshooter gadgets, he fails, however. Spider-Man needs to use Wolverine's powers, but claws are essentially extra limbs so they just go wild as he's trying to process how to use them, and ends up stabbing himself just offscreen. (The cartoon cuts ahead citing technical difficulties.)
In Equestria Girls, Twilight takes a while to learn to walk on two legs and utilize her fingers after turning human.
The season 4 premiere starts out with Twilight Sparkle learning how to fly with her new wings with mixed results. Later in the two-parter, she is able to fly from one city to another with Spike as a passenger but not without him kissing the ground afterwards.
In "Power Ponies", the cast gets sucked into a superhero comic and receive super powers. When they first confront the villain they utterly fail to use their powers effectively. Over the course of their episode they learn to get it together.
In Twilight's Kingdom Part 2, Twilight has to raise the sun and lower the moon now that she has Celestia's and Luna's magic. It's a bit shakey, but she manages.
The Adventures of Prince Achmed kicks into gear when Prince Achmed mounts a magic mechanical horse and pulls the lever that makes the horse fly. He does not know how to make the horse land.
In Beast Machines, the Maximals initially have no idea how to transform into their more combat-capable robot modes after the Oracle alters their bodies to make them more technorganic. The on-board computers their original bodies possessed that handled transformations for them are absent, meaning there's more to it than simply saying "Maximize". It takes a Die or Fly situation for Optimus to figure it out. He later teaches the other Maximals how.
Truth in Television: Many people have the power to do certain things but often lack the skill or training to do so.
Learning to use a gun is often very much like this. Sure, there's the obvious parts such as pointing the barrel at what you want to kill and pulling the trigger. However, mastering a gun, especially a complex modern assault rifle, is difficult. You have to learn about sighting, trigger pull technique, the fire control group, loading, dropping magazines, changing magazines, aiming, disassembly, reassembly, and cleaning.
Originally part of the attraction of firearms was that any idiot could be taught to use one in a couple of months or less, while mastering a longbow or even a crossbow would take far longer (traditional longbows actually demands a lifetime of training, because you NEED to have started using one regularly in your youth to develop the muscles necessary to draw it). Firearms, in their infancy, were wildly inaccurate due to being little more than tubes containing blackpowder, an ignition source, and a metal ball for which the blackpowder would propel into an enemy, so back then "mastering a gun" did boil down to "point, shoot, and hope you kill something". Longbows were still considered deadlier than the musket because they were accurate AND could definitively kill in the hands of a skilled archer (the arrow having much more penetrative power than a metal ball tumbling through the air). With the advancement of firearms into assault rifles, sniper rifles, machine guns, smgs, etc, guns managed to reach and surpass the killing power of bows, even with all the extra mechanisms that allow for such advancements. While maintaining and using firearms now is much harder than before, it is still far easier than trying to master a bow for combat purposes.
Many martial arts are good examples. Throwing a punch? Simple, right? Wrong. Each martial art has a technique, and it takes time to learn how to punch properly. Same applies to strikes, kicks, throws, stances, et cetera.
To wit, one of the most common injuries in martial arts (but mostly boxing) is known as the boxer's fracture and is caused by poor punching technique.
Somewhat inverted with building a PC: the standards of interconnects (everything is designed to fit one way) and mounting (everything is designed to mount one way) make the physical building of a PC no harder than assembling that Lego castle. The hard part is troubleshooting when something goes wrong or making sure it all fits together. It is true that most incompatible parts will not fit where they shouldn't go, but that doesn't help when you end up with a computer with no RAM because the sticks you ordered won't fit.
The software side is where the real "fun" begins. Software has become so user-friendly that the average user might think that loading up a computer is as easy as installing an "app". However, if the computer does nothing but beep at you when you power it on, you had better know what "beep codes" are. And while modern OS's have simplified the process of installing any drivers you need, your initial capabilities are still limited to whatever the OS disk has built-in support for.
Lucid dreaming can be like this sometimes: you know that (at least in your dream) you're a Reality Warper, but you can't figure out how to actually do anything with that.
Walking. Of all animals, humans are the most inept at moving around immediately after being born. Of course, there are many reasons for this.
Having a bipedal gait limits the size of the mother's hips, meaning that only a small enough (and therefore weak) baby can be born.
A proportionally sized brain wouldn't fit on the way out, so infants sacrifice developing the neurological control of their bodies until after they are born in order to reduce their skull size.
A bipedal gait also means that each of a baby's limbs has to be twice as strong as those of a quadruped of the same mass in order to lif his/her weight.