Carly has the ability to read minds and doesn't suffer from the flux of thoughts she's bound to be hearing every day like most telepaths do.
Sam has superhuman strength, and while not Nigh Invulnerable, her stamina and endurance are increased to the point where Carly, while borrowing her power, was able to do two hundred push-ups in one sitting. Her lack of invulnerability comes out when she gets hospitalized for a stab wound.
Discussed in the seventh episode of Sailor Moon: Legends of Lightstorm. Sailor Mercury tells Sailor Mars that her rocket-propelled speed is not a viable combat option because she's not a speedster, and therefore doesn't have any of the secondary powers required to use super-speed in close quarters (because of this, Mars always fights inertia and g-forces when running at high speeds, and therefore is forced to make very wide turns).
In The Danny Phantom Superhero Project, Danny got his powers from Jazz, who then started selling temporary powers to would-be villains to fund her research. When Danny discovered this, she gave herself Super Speed in order to get away, but when she tried to spin around on her left leg, all the cartilage, tendons and ligaments from her knee down disintegrated from the sudden g-forces. Word of God says that he was always confused by how speedsters like the Flash could corner like that.
A problem with regeneration was mentioned at least once in Fan Fic:
"We had learned the hard way- well, Steve had learned the hard way, by having it happen to him; Valerie and I had learned the easy way, also by having it happen to him- that while werewolf bodies heal wounds instantly, they don't always heal right."
A Fantastic Four 2099 fanfic series occasionally explored the limitations of the characters' abilities in this way:
Johnny Storm (or rather, his clone — all of the Fantastic Four of 2099 are clones of the originals) is at one point exposed to the Negative Zone's poisoned atmosphere through a leak in a labor frame suit he was wearing/driving. He ended up briefly coughing from it, but otherwise he sustained no long-term effects from it. When questioned about this later, he pointed out that as The Human Torch he tended to be surrounded by plasma flame, meaning that the very air he inhaled was superheated plasma. His lungs would have been scorched without the Required Secondary Power of enhanced lungs that could very efficiently filter out what he breathed. As a result, breathing toxic Negative Zone air was relatively a piece of cake, and he was shown doing so without a gas mask on at least one occasion.
On the other end of the spectrum, the clone of Ben Grimm has the same rocklike epidermal layer as his predecessor — which he at one point described as "a full-body callus strong enough to withstand being hit by a missile." Unfortunately, his thick hide was still pierced on a few occasions, but the injuries were slow to heal, leaving deep craters and sensitive scar tissue in their wake.
In Minsinoo's Climb The Wind, Logan mentions that he has increased protein needs as a result of his healing factor. Also that he's not good at dealing with chronic pain, because he's used to things healing almost instantly.
Washuu restores Luna's ability to turn into human form. Later we learn she also retained cat's muscle density, which makes her really strong and agile but also uses proportionally more energy. So she either has to eat a lot in human form or stay most of the time as a cat to save energy.
The protagonist receives a strength multiplying bodysuit, and learns the hard way it lacks any kind of reinforcement (he forgot to read the manual, then punched a wooden pillar breaking his wrist). Fortunatly he still has medical nanites, but those too use a lot of fuel while healing major injuries. He stillhasn't been able to read the manual.
At the very end of With Strings Attached, we find out that the cloned bodies that the four are inhabiting had been supplied with complete immunity to disease to prevent them all coming down with dysentery two days after arriving in Focan, which was quite filthy.
Also, Jeft talks to himself about all the stuff he had to build into Paul to get him to work properly:
~Now, I gotta say, I did a darn good job on him. Probably a good thing I didn't tell Shag and Varx that he only had about a forty percent chance of remaining stable after he came back together, with all the weird scalar/planar energy fields I had to design into him. They just don't have any idea what you have to go through to get a human-sized frame to be able to wield that kind of strength and still walk without creating giant holes or move his arm without blowing down everything in its direction. I still couldn't get it perfect, so he's always gonna make some chaos if he's not careful, but jeez, I was brilliant, converting most of that kinetic energy right back into raw Field energy before it even got past his skin.~
Harbinger mentions this in regards to Shepard'sPsychic Powers that allow him to move at Super Speed. His fists move extremely fast when he strikes someone in close quarters, hard enough to crumple armor and throw people across the room, but his arms also move so fast and with so much force that they'd break on impact. His armor and omnitool generates a dual-layer mass effect field (pun questionably intended), with the outer layer being a hardened kinetic barrier while the inner layer being a "cushion" that behaves like ballistic gel, absorbing the reaction to his punches.
In Blood and Fire, the Citadel races know the science behind Covenant plasma weapons, but they lack the material science and power generation knowledge to make the things work in a practical, combat-useful package rather than in the laboratory.
Star Trek and Babylon 5 fanfic "Task Force 43" lampshades this viciously when the Vree attempt to blackmail the Federation into accepting them into the Federation under threat of proliferating warp technology to the local races. To counter the blackmail, the Federation ambassador hands out data crystals containing basic information about warp technology (Roughly equivalent to what Cochraine had during his first warp flight). What they do not give, however, is Federation anti-matter energy production technology, which is the only way to produce enough power to sustain a warp field for a ship larger than a small fighter.
In The Universiad, OSR augmentations are so powerful that Power Limiters are needed, with many careless operatives destroying themselves from careless use.
In the Lunaverse, Trixie's invisibility doesn't work against Octavia because not only can the latter hear the sounds the former is still making, she can also hear the inappropriate absence from a silencing spell. By the time At the Grand Galloping Gala comes by, Trixie has come up with a way around the problem.
In An Anthem For Sheltered Bays, Eren, being a mermaid, has eyes light-sensitive enough to see in the dark and greater upper body strength to make up for a fish lower half.
In chapter 34 Smuggler points out that while he could easily recreate the electronics and materials needed for the airbursting explosive rounds, the software and targetting computer needed to make them work right isn't so straightforward, not something he can create in the short time available.
Alexandre's nanoaug armour doesn't completely nullify kinetic transfer, meaning that Ursus can stun him with a strong enough punch to the head.
In Shatterheart while R!Syaoran can replicate his clone's fighting style and abilities by learning through their shared eye, R!Syaoran has a slower reaction and doesn't fight as well because he didn't actually learn it himself.
In Weaver Nine, the Society has a cape called Heavenly Fist whose power is the Megaton Punch. Unfortunately, while it does send targets airborne intact, it doesn't cushion the touchdown or slow the descent phase. As a result, anyone without Super Toughness gets turned into a bloodstain on arrival.
In the Stardust sequel Mente MateriaMatt'sSuper Reflexes don't come with a boost to his physical speed, meaning he can see things happen but can't physically respond to them in time. He can activate his magic though.
A fairly common idea in Sasuke- or Kakashi-bashing Naruto fanfics is to point out while Kakashi used the Sharingan to copy the taijutsu Lee used against Gaara so Sasuke could use it in his fight against Gaara, Sasuke has not had the years of physical conditioning that Lee has to back it up, thus making it less effective (while in canon it worked rather well). Also common is Sasuke trying to copy the Shadow Clone technique without realizing he doesn't have the vast chakra reserves that Naruto needs to perform it.
Gamer's Mind protects Jaune from getting overwhelmed by all the input he gets from his Super Senses. Reinforced when Gou uses Clairvoyance in "Believing" and finds the added input 'disorienting and dangerous to use in a fight'.
In "Faces" Jaune explains in detail why trying to use illusions to make one appear bigger or smaller is very difficult - there are so many little details one has to get right. Applying illusions on others is also difficult, even with Aura to massage some of the fiddly bits.
Acceleration is Time Mastery applied only to Jaune, but not to his Elementals or allies, which means he can't use them as effectively while he's sped up. Also, spending all that time while dilated means he's physically older than the calendar would suggest.
Tenne's ability to guide projectiles using his eyesight is disrupted when he blinks, and training and experience only go so far in trying to counteract this natural tendency. When Conquest infects him, he gains many more eyes, and unblinking Grimm ones at that, making him much more effective.
In "Homecoming", we see how many things Jaune has to do in order to be stealthy. It's not enough to use Delusory to bend light and hide himself visually - he needs to control air to prevent sound leaking or unwanted wind motion, control heat to prevent the air from heating from friction as he moves at Super Speed, and harden the ground to prevent it cracking under his Super Strong footfalls.
Some of the Skills Jaune learns explicitly don't provide their user with any protection should they backfire on him.
In "Examination" Jaune notes that Aura doesn't increase mass or provide additional anchoring. In high-level combat, even if an attack doesn't deal enough damage to noticeably deplete Aura reserves, it's still possible to have someone Blown Across the Room.
Quite a bit of the fic is dedicated to discussing the need for Taylor to gather resources and develop appropriate tools and subsystems in order to recreate the technology Tony had.
Defied with the mass production Iron Legionnaire suits. One of the key selling points Taylor offers to the US Army is the fact that they don't need special training to maintain or operate, which cannot be said for most Tinkertech. This is explicitly demonstrated when she rejects the top pilots the military intended as testers in favour of ordinary line troopers, who still manage to quickly learn the ropes anyway, then offers a suit to the motor pool to fiddle with. No matter what abuse it gets put through, it still remains within the ability of non-superpowered mechanics to work with.