Alternity specifically limits the degree to which muscles can be augmented with cybernetics by specifying required secondary cybersystems that need to be installed first. Want to get a single point of extra strength? You need a nanocomp installed to manage the synthetic myomer. 2 points? Need a nanocomp and you better have endo or exo skeleton to mount those hyperstrong muscle fibers. 3 points? Nanocomp, exo/endoskeleton, AND your limbs better be fully cyberized, because your poor meat self is going to pull itself apart otherwise.
The Traveller system has a detailed set of rules about psychicteleportation, its energy limits, and how 'porting to different altitudes and different areas of planetary rotation can produce fever or hypothermia, depending on whether the jumper is gaining or losing energy.
Godlike allows players to reduce their power costs by not taking the prerequisite powers. The background material includes many examples of characters who lack prerequisite powers or whose powers have significant drawbacks, and one of the major themes of the game is finding ways to make these characters militarily useful despite their limitations. One example is a character who can teleport without being able to control his destination; He becomes a propaganda tool by spreading Allied graffiti all over Europe.
GURPSnotes the need for various secondary powers. In some cases the secondary powers are implicit in the ability and their lack has to be added through disadvantages and limitations, other times explanations about what is realistic and what isn't are given (along with ways to justify getting around them) and finally the designers point out that justifying powers isn't in the spirit of some genres.
Notably in GURPS Supers, there is a Costume advantage, which must be purchased if you want your costume to automatically work with your powers. It isn't technically "required", but they note that many super powers would leave the user naked without it.
In Aberrant, Novas are generally assumed to have these unless explicitly stated. The in-game explanation is that they subconsciously develop these additional effects alongside because they believe powers should work in certain ways. For instance, a mega-strong Nova trying to lift an oil tanker believes the tanker should be lifted intact, and subconsciously wraps a "quantum field" around it to keep it intact. The same field is nowhere present when he smashes through a wall.
A fairly common form Aberrations can take is the loss of RSPs. Alternatively, a few upgrades give you RSPs, for a certain value of "required". For instance, Bull in a China Shop is an Aberration that ruins your fine control over your Super Strength. Unbreakable is an Enhancement to that quantum field to let it affect your weapons so that your sword doesn't bend or break when you use it with an arm that can shatter steel.
One sourcebook introduces a sneaky attack power (Disimmunise) that works by shutting down other Novas' secondary powers, causing them to fall victim to the side effects of their own powers.
In both games, vampire characters can gain an ability called "Auspex", which at its lowest level grants heightened senses. Unfortunately, while the vampire in question is using the heightened senses, they can very easily be overwhelmed by all of the stimuli.
The two games also have Celerity, which is super speed and it's stated that no matter how fast a vampire moves, he'll never catch fire and so on. So, basically A Vampire Does It. They actually say this, very clearly. Celerity is a supernatural power. It doesn't make you faster by enhancing your reflexes or something, it actually is a magical manipulation of space and time.
Likewise, use of the "Obfuscate" discipline functions more as a mind trick rather than true invisibility, so there's no need to worry about the Vampire being unable to see.
The "Lure of the Flames" path of the "Thamaturgy" power gives the vampires who have it a limited immunity to fire in that they cannot be harmed by the fires that they themselves have conjured as long as that fire is still in their hands. As soon as they let it go, however, it can burn them just as easily as anyone else.
One specific aversion is pointed out in Requiem: a Blood Magic ritual that fills the caster's veins with acidic poison to deter neck-biters. It's perfectly safe for vampires to cast, but they can also teach it to their blood-bound human Ghouls... who, if they use it, react exactly as humans do when their veins are filled with acidic poison.
In the Spanish parody of The World of Darkness, Fampiro (Fanpire), one of the powers available to the "Fampires" is Super Speed, which damages the user due to friction. But this is the only power with any drawback, since the power of super-strength doesn't damage you if you don't have the power of super-resistance, nor will the body-manipulation power damage or kill you if you miss ("Don't touch that heart too much").
In Mage: The Ascension it's explicitly stated that any Mage using Forces to bend light in order to make themself invisible cannot see using normal vision and needs to actively use secondary spells in order to see. Fortunately, most Mages will have other options available, including but not limited to using Forces to see infra-red, sensing the Matter around them (although they'd still be liable to walk into a tree), or using Mind magic to see through another person's eyes. Or use Correspondence 1 and just cast their senses around them.
The paradigm system can add or subtract required secondary powers pretty dramatically. An animist mage that believes that photons and other particles are sentient beings that can be negotiated with could easily cast invisibility without losing his own vision, because he's just asking the photons to keep his secret. But this might add another required secondary power (well, spell) because he now has to talk to the photons constantly while invisible and needs another effect to silence the sound.
Magic: The Gathering's "wish" cycle shows several people wishing for skills, items, or powers from Djinn, with the flavor text noting that they neglected to wish for abilities that would let them properly utilize those things.
Golden Wish:She wished for nobility, but not for a nation to honor it.
Cunning Wish:He wished for knowledge, but not for the will to apply it.
Death Wish:He wished for power, but not for the longevity to abuse it.
Burning Wish:She wished for a weapon, but not for the skill to wield it.
Living Wish:He wished for growth, but not for a way to control it.
In Scion, the most basic power available from any given Purview is usually the required secondary power needed for the rest of the powers to either work as intended or work as intended without killing the user. For example, the first dot in Fire and Frost makes the user immune to heat and cold, the first dot in Water lets the user breathe underwater, the first dot in Sky makes the user immune to falling damage, and the first dot in Death lets the user see and interact with ghosts.
The books actually lampshade and handwave it with Epic Attributes, which allow supernatural and divine beings to be super-strong, super-fast, super-resilient etc. Due to the way the Scion universe works, and due to the fact that all supernatural beings are bound by Fate, which represents (to a point) the collective subconscious of humanity, beings with Epic Attributes physically act not like they scientifically should, but how the common person thinks they should. The common person doesn't know that it's impossible to lift a bus without breaking it no matter how strong you are- so a demigod with Epic Strength can do that.
Scions can even turn this on and off at will. Normally, Epic Dexterity-granted Super Speed has no issues with sonic booms or friction - but if a Scion wants to run down the street, shatter every window present with their sonic cone, and then use the broken glass to cut Titanspawn to ribbons, well, make an attack roll.
Part of the reason Warhammer 40,000 contains such nightmarish procedures to convert a normal human into a Space Marine is due to attempts to provide them with Required Secondary Powers. In order for a Space Marine to move their Power Armor as swiftly and instinctually as their own body a plastic film fitted with neural sensors and interface points is inserted under their skin, to allow them to interface with it directly. In order to prevent their bones from snapping due to the immense forces created by the Power Armor's servomotors they are reinforced with various chemicals, such as ceramics. In order to provide the chemicals necessary their organs are modified so that the Space Marine can digest concrete and metal. And so on and so forth.
This is a debatable point. It is true that Space Marines need to be modified in order to use their power armor, but unlike some settings, there is power armor available for normal humans. It's difficult to say whether Space Marines are modified to use their equipment or their equipment is specced for the modifications made to Space Marines. Almost every piece of equipment they use has a variant that can be used by normal humans.
It can be argued that the augmentation is a required *tertiary* power, since without both the natural strength boost in conjunction with the power-armor's strength boost, they would be unable to carry and fire the unreasonably large guns they are issued. Man-portable Las-cannons and Multi-meltas, weapons that weigh 40+ kilos and are usually crew served or vehicle mounted weapons are carried around by Marines and fired from the shoulder.
Sisters of Battle, who are just regular women without any kind of super-strength, are able to carry around multi-meltas and heavy bolters with their power armor. It's worth noting though that the model of Sisters carrying theses heavy weapons seems to have their left arm (which, given their pose, is the one doing most of the lift) reinforced by something that looks pretty much like hydraulic cylinder.
At least half of the powers of the implants (instantly sealing wounds, ability to withstand Explosive Decompression, super-dense bones and auto-hypnotic Suspended Animation among them) are there to ensure the survival of the Marine when all of the Power Armour and other defenses fail. Because they take that much effort to create that their creators wanted to ensure anything short of an anti-tank round wouldn't stop them.
One of the reasons that Space Marines can only be made from adolescent children is because a large part of those implants affect hormonal growth. This is because a large number of them affect bone growth and organ development, which stops after adulthood. Even then, they need to find suitable specimens for implantation, as even a healthy adolescent male can still reject the organs and devolve into a feral beast. Kor Phaeron, foster-father of Lorgar, was too old to become a space marine specifically because of this, and to keep up with the rest of the Word Bearers he had to get several augmentation surgeries and a specially-made suit of cataphractii terminator armor to join them. And even then he's still considered sub-par compared to true astartes, a fact that most of the legion resented him for (he only retained his position due to nepotism).
Scrouges are winged Dark Eldar. To become one first requires a bone hollowing surgery to help them become light enough to fly. A very, very, VERY painful surgery.
Human psykers, on the other hand, lack the secondary powers to contain their own abilities. The Imperium is able to mitigate it with extensive implants, but only to an extent. Any human psyker possessing Beta-level or higher powers is thus insane and very likely to call down Perils of the Warp. Averted with the Eldar, who do have the technology to safely employ psyker abilities. Their Dark Eldar kin avoids psykers specifically because they no longer have the technology to safeguard against perils (especially since their hedonistic lifestyle actually draws the warp closer to them, and without soulstones there is no fate worse than death for them), as a consequence that they field no psykers whatsoever despite being one of the most highly-sensitive psychic races.
Anyone who wants to master chaos and become a Daemon Prince must have the willpower to do so. It's explicitly stated that Chaos will grant you any power regardless of your standing, but if you do not have the willpower to control it, the gifts will consume you and turn you into a writhing mass of flesh and sinew.
The Orks were engineered to be the perfect warrior race, to the point that a single Ork is enough to start and end an invasion. This is in large part due to their biology; Orks reproduce via spores which do not just spawn orks, but also Squigs and Gretchin. Gretchin help build settlements and weapons while Squigs provide everything from fuel to labor to food. Orks themselves also have a gestalt psychic field separate from all others, which is implied to help with their own technology, ensuring Orks will always have the weapons they've become accustomed to culturally at their disposal. All of these are required for Ork Society, otherwise how else can you explain a bunch of greenskinned hooligans going on an intergalactic violent pub crawl, and winning?
Orks also have some latent, subconscious Reality Warper powers, which explains how their haphazardly assembled technology actually works. "Red goez fastah" becomes a thing because the Orks have a fundamental belief in this. One story relates how a squad of Imperial Guardsmen were pinned down by an Ork Boy with a heavy machine gun. When they finally killed it, the Guardsmen took the time to examine the weapon, only to discover it was effectively a weapon-shaped box of random metal parts that shouldn't have even chambered a bullet, nevermind fire one.
The Tyranids come in with some of the most biologically horrifying examples. Because of the nature of the swarm, any secondary "power" deemed unnecessary is discarded. This results in creatures that are horrifically efficient at killing and genetically simple to mass produce on a galactic scale, but have no digestive systems to speak of whatsoever. The lack of the majority of internal organs instead make them insanely hard to put down, even though they are technically running around naked, as their bodies are largely reinforced bone and muscle. The biggest user of this trope is probably the Zoanthrope, psychic creatures that have since atrophied their bodies to the point that they must levitate themselves via their own psychic powers. Without it, their bodies likely couldn't even support itself. It's likely that the Hierophant Biotitan uses a similar method from suffering from the Square/Cube Law.
Wild Talents Second Edition's One-Roll Talent Generator table gives a character with any level of Flight above the minimum Light Armor, "'cause honestly, at around 500 mph, you're going to need to worry about skin abrasion if not an air supply."
In Shadowrun super-strength cybernetic replacement limbs are specifically noted not to have these — a recipient trying to lift a car is in danger of ripping his prosthetic limbs off instead.
Cyberpunk similarly discusses the limitations of cybernetics, again using a replacement arm as an example: You could not throw a car with it alone, but you could, for example, hold on to a ledge for a long time.
In Rifts there's a class known as the Titan Juicer, chemically-enhanced humans who are much larger and stronger than is otherwise possible for a human. The class specifically mentions that the bones are made stronger so as to handle the increased weight and strength. Their punches are also so powerful they have to wear special gloves so that they don't break their hands when they take a swing at something.
Teleport in D&D 3.5 has some notable limitations, such as you need to have some idea where you're going (the less familiar you are with the target, the more chance there is off ending up off-target, albeit safely... or getting "scrambled") and being limited to 100 miles per level (900 miles at the minimum level to cast it). Greater Teleport, on the other hand, can take you anywhere within the same plane of existence.
A much more prevalent meta D&D and Pathfinder example from multiple editions: being a player character apparently gives one the extraordinary ability to precisely estimate the range of distant objects and determine which are and are not going to be affected by a large area of effect spell which goes off, all when done in very brief combat rounds. Alternatively, the precise ability to determine whether one can reach the current target before the target recovers from their current action. Since the games are played on a grid or other battlefield, and the range of everything is given in very explicit terms, the players have no problem measuring whether something will reach or counting squares and determining exactly what is and isn't a set distance away (and this affected or in range). There's no justification for their characters having the ability to instantly see which targets moving along a chaotic battlefield are exactly within range or not.
All dragons in D&D have complete immunity to whatever damage their Breath Weapon inflict. A necessity to avoid their innards or their maw suffering when using this redoutable weapon.
Mutants & Masterminds largely avoids this, viewing it as Acceptable Breaks from Reality. For example, a character can have Super Speed that only takes the form of them being able to run really fast, without having any kind of durability power (though they'll want one if they plan on crashing into anything), or being able to perform normal tasks at faster speed (the Quickness power, which delegates this, is separate), or being able to react faster than normal (Improved Initiative), or even being able to attack multiple times in one turn (Multiattack or Area Attack). Most players planning on playing a speedster will take Improved Initiative, Multiattack, and Quickness anyway (if only to fit the theme), but there's nothing stopping you from having just really fast running. The designers themselves acknowledge this, because it's how Super Speed tends to work in comic books anyway, and a more "realistic" portrayal of a speedster would be totally overpowered.