Somehow, somewhere, something went horribly wrong on a cosmic scale.
Maybe it's a Negative Space Wedgie. Maybe the Butterfly of Doom flapped its wings once too often. The point is, the universe isn't behaving as it should, and this is not a good thing for our protagonists. Whatever the "flaw" is will almost always be very vaguely defined, but whatever it is, it's almost always causing the world to become more crapsack. If the "error" is personified, it will usually be an Eldritch Abomination. Correcting it may be a goal of the protagonists, but sometimes whatever it is is so far outside their ken that it's untouchable by them.
Contrast Cosmic Keystone, something necessary for balance and stability in the cosmos. The Cosmic Flaw may have been created from weakening or removing said keystone, the result of a Reality-Breaking Paradox, or The Death of Death. The Reality Warper may fix or cause this. May sometimes happen because God Is Flawed and He made a mistake. The Cosmic Flaw may involve Merged Reality and/or All of Time at Once.
- The Idea of Evil from Berserk works something like this, with the twist that it was actually created by humanity. Essentially, human belief that there must be something wrong with the universe for the concept of suffering to exist caused this Eldritch Abomination to be Clap Your Hands If You Believe'd into existence for the express purpose of being that wrong thing.
- Highschool Dx D: In volume 3, an enraged Kiba unlocks the Balance Breaker form of his Sacred Gear "Sword Birth", and performs the impossible act of creating a holy sword out of demonic energy. This confirms some of the older characters' suspicions that both God and Satan are long dead, and the laws of reality are no longer operating as intended. In fact, Sacred Gears (originally created as a way for God to empower human champions) were never intended to be Evolving Weapons at all, and the ability of some of them to kill gods is likewise a relatively new development.
- In the Emperor Joker arc of Superman stories, the Joker has tricked his way into receiving Mxyzptlk's reality-warping powers and remade the world in his image. Some people, primarily Superman, feel that there is something fundamentally wrong with their new reality. As they meet more powerful beings resisting the Joker's influence, it is revealed that as he pulls more and more strings, Joker will begin unraveling the very fabric of existence.
- Grant Morrison seems to enjoy these.
- The Big Bad of his Batman run, Doctor Hurt, claims to be "the hole in things" and "the piece that never fit." It's eventually revealed that he's not quite that bad, though he is a Humanoid Abomination.
- Darkseid becomes one of these in Final Crisis; after his body was killed by Orion, he fell back in time and became a "black hole at the base of creation" that threatens to consume the entire multiverse. The series' other villain, Mandrakk, can be thought of as a metatextual version of this, as Word of God says he is essentially the personification of negative trends in the comic book industry itself.
- In the Grand Finale of his New X-Men, set in a Bad Future, the Stepford Cuckoos make frequent reference to the fact that reality wasn't "supposed" to have gone down that path, and that there are "holes" in existence. In the final issue, the "hole" is revealed to be Cyclops quitting the X-Men; the Phoenix, which "burns away what doesn't work," sets things back on track.
- This is the whole premise behind the mega-crossover fic The Infinite Loops. Yggdrasil, the world tree, is actually a gigantic computer and each of its branches is a different reality, and it so happens that that computer has crashed; so badly that the gods - better known as Admins - are trying to fix it and the only way to buy time is to have people in the various settings repeat their lives over and over and over again. And yes, the system is susceptible to viruses.
- We Are All Pokémon Trainers:
- Glitch Pokémon as a whole, while not necessarily malevolent, are living flaws in the universe capable of warping it around them.
- When the Mobius Society interrupts a ritual led by Sol and Ton, as part of their plan to fuse all universes which kickstarts the Entralink Arc, a crack is left in the sky as a result of the multiversal disturbance, and beings from all over the multiverse start showing up.
- In Dogma, reality as we know it hinges on God being infallible. In short, you can't prove God wrong because doing so would end the world. Which becomes a driving force in the plot when fallen angels plan to use a loophole in Catholic dogma to overturn their banishment.
Metatron: If they get in, they will have reversed God's decree. Now, listen closely, because this bit's very important. Existence, in all its form and splendor, functions solely on one principle: God is infallible. To prove Him wrong would undo reality and everything that is. Up would become down, black would become white, existence would become nothingness. In essence, if they're allowed to enter that church, they'll unmake the world.
- In Time Bandits, the dwarves are using holes in creation to leap through time and space as robbers. It leads ultimately to bad things for them.
- The Belgariad: Basically, a star died in the wrong place. This caused a chain reaction that destroyed an entire galactic cluster outside of schedule. The result was that the purpose of the universe, the force of destiny, was divided into two opposing awarenesses. The contention between them causes everything that happens in the series.
- This is the basic premise of The Dark Tower: The titular Tower is the center of all existence, and it is starting to malfunction, which causes the different realities to drift, blend, and intersect at random intervals. Thus, the main characters are on a quest to find the Tower and repair whatever is wrong with it.
- Near the end of Death's End, it's revealed that the early universe consisted of ten dimensions rather than three, and the speed of light was near-infinite. Unfortunately, over billions of years Sufficiently-Advanced Abusive Precursors have been using incomprehensibly-advanced weapons to create Negative Space Wedgies that are reducing the dimensionality of the universe, and the speed of light itself, to destroy their enemies. Eventually the universe will be reduced to two dimensions, and then one, and then... well...
- In Elantris, the catastrophe known as the Reod basically inflicted The Magic Goes Away in the mage-city of Elantris, turned the demigod-like inhabitants into zombies and created a huge chasm just for good measure. It turned out that the new chasm caused everything, since the Elantrians' Hermetic Magic is based on the country's geography, which the chasm's appearance altered.
- In Funny Business, when Jeanette is upset about her poor performance in a math test, she alters mathematics to make the answers she gave the correct ones - physics soon follows suit, and a black hole approaches the solar system.
- Doctor Who has the Time Cracks, which are cracks, in time, that obliterate people and things from the timeline when exposed to them. In "The Pandorica Opens", it's revealed that these cracks were formed from the TARDIS exploding after hitting a burst of time energy and overheating, but what caused the burst in the first place is never directly explained.
- In The Hitch Hikers Guide To The Galaxy, Ford Prefect and Arthur Dent find themselves two million years in the past of Planet Earth — which is a massive supercomputer devised, at mind-boggling-cost, to figure out the Question to the Answer of the existence of lifekind. Arthur realises they are at that point on the program where discovering The Answer is imminent. The Answer is of course Forty-Two. By a feat of lateral thinking, they discover the Question.
What do you get if you multiply six by nine?
Six by nine. Forty two?
That's it. That's all there is.
I always thought something was fundamentally wrong with the universe.
- The backstory of Demon: The Fallen describes the original universe as a perfect machine, with every natural law, concept, being, and atom humming together in harmony and beauty without parallel. The one flaw was that mankind seemed... unable to gain sapience on their own. Long story short, God got angry that Lucifer forced the issue by giving mankind sapience, and so God "brushed" the world with his presence, which was the equivalent of hitting a car with a wrecking ball. Sure, the universe survived, but in a broken, imperfect and continually decaying state that can't ever self-repair to its former state.
- The Elder Scrolls:
- The series has events known as "Dragon Breaks", which are this trope crossed with a Time Crash. Essentially, the draconic God of Time, known by many names but most prominently as Akatosh, is "tampered with" so to speak, causing him to temporarily "forget" the true course of historical events that happened for a brief period of time. As a result of this, all possible events that could have happened during that time, even mutually exclusive ones, will happen, though they might not have happened "fully" either, so to speak. They typically involve mortals attempting to use something of divine substance and cross over with Reality Is Out to Lunch. This most prominent Dragon Break occurred in the 1st Era, when the Maruhkati Selectives, an extremist sect of the already extremist anti-elf Alessian Order, carried out a ritual in attempt to purge Akatosh of the elven aspects of the mythological basis that Akatosh was based on, the Aldmeri golden eagle god, Auri-El. For the next 1008 years, during an event that came to be known as the "Middle Dawn," bizarre and impossible events occurred during this time; people gave birth to their own parents, some sources mention wars and major events which never happened according to other sources, the sun changed color depending on the witness, and the gods either walked among the mortals or they didn't. How could they measure that period of time? They used the phases of Nirn's moons, said to be Lorkhan's decaying "flesh divinity", to measure time as they were not affected by the event. Even the Elder Scrolls themselves cannot rationalize the conflicting events of the Middle Dawn. When the Scrolls are attuned to that time period, their glyphs are said to simply disappear.
- Dagoth Ur, the Big Bad Physical God of Morrowind, is essentially a living Cosmic Flaw. He's using the divine powers he channels from the heart of a dead god to twist his followers into Body Horror abominations and spread a magical disease. Further, very much steeped in dream-imagery as he "sleeps awake" at Red Mountain. "The Dreamer Is Awake" is often found scrawled by the mad cultists in their strongholds. To further get into esoteric "lore speak": The implication is that Dagoth Ur has discovered an unspeakably dangerous middle-ground between CHIM, Amaranth and Zero-Sum where he exists in a godlike state because of his awareness of Anu's Dream but, unlike CHIM where he exists as one with it and maintains his own individuality, Amaranth where he exits the Dream to make his own, or Zero-Sum where he simply fades into the Dream, Dagoth Ur's twisted, traumatized and broken mind is being imprinted on the Dream of Anu. Through Corprus, the manifestation of Dagoth's will, he is turning Anu's Dream into his own.
- Fate/Grand Order: The "Singularities" are occurrences in certain locations and time frame, where the history of the world is being threatened (usually due to an outsider's interference). The prologue has the protagonist being sent to the Singularity in Fuyuki, 2004 AD to fix the events within, before 7 other, bigger Singularities appear; thus the quest for saving the human history - the Grand Order - began. In the end, the Singularities are corrected, and the Big Bad behind them all is defeated; but some time later, 4 smaller Singularities pop up and the protagonist has to fix them too.
- Mega Man Battle Network presents virtual versions:
- The Final Boss of the 2nd game is a living aggregate of computer bugs that come to life and threaten to overload the Internet's servers called "Gospel".
- The Final Boss of the 3rd game is the faulty "alpha" version of the Internet that, when released, threatens to consume the whole current internet like an amoeba, aptly named "Alpha".
- In the Myst series, different worlds, or "Ages", are basically written into existence by describing them in books, and they can be flawed, even fatally so. Riven had a "star fissure", a big crack in the ground that opens to space, and when ruptured, it sucked the whole Age into it.
- According to Word of God from the makers of Shin Megami Tensei, a flaw in the universe turned God evil. No more detail has been given, and indeed the "flaw" has never been mentioned in the games themselves, which has led some fans to speculate that the statement was an I Meant to Do That designed to make the games more appealing to Western audiences.
- Wandersong: The world is ending and it's because the overseers are becoming corrupted after living so long.
- Awful Hospital: The villains are Invoking this trope by attacking the fundamental concepts of "sickness" and "health" across The Multiverse of the Perception Range. The Hospital, which embodies the concept of medical care, is falling apart, while Earth suffers a full-fledged Zombie Apocalypse. This turns out to be an Assimilation Plot to subsume the entire Range with an impossibly virulent "alpha malady", using the heroine's infant son as the main infection vector.
- The main ongoing plot of Goats, when it remembers to have a plot, revolves around the heroes trying to fix the buggy software code which the multiverse runs on. If it's left unfixed, all of existence will crash on December 2012.
- In Homestuck, it's revealed that the creation of our universe was rushed and mishandled (they were on the clock and one of the people who were supposed to do it didn't want to), and as a result, it has cancer, which apparently comes in the form of Physical God Big Bad Jack Noir.
- The titular misfile in Misfile- an error in reality that changes the lives of several people. Subverted however, in that most of the affected people's lives have improved because of it, and the only person who really considers it a problem is Ash.
- The Order of the Stick: The Snarl, which was created due to the gods' disagreement of how the world should be. After the Snarl destroyed their world, they created another world to contain it, but this new world was not perfect either, and over time cracks ("rifts") started to appear in the fabric of reality. This has happened billions of times, because the gods who created the Snarl had four "quiddities" between them, but it immediately slaughtered the Eastern Pantheon, the only source of green quiddity — meaning that it is literally the realest thing in existence, as every world created to contain it since then only had three.
- In Schlock Mercenary, at one point there was a minor distortion of teraport mechanics...which turned out to be a symptom of the Milky Way being pinched off into its own little universe, and then slowly destroyed from the inside out. It came very close to destroying the whole galaxy, and would have if if it weren't for a bizarre loophole in the physics of the anomaly.
- In Fine Structure whenever a "super science" is used a few times the Imprisoning God erases the science from the universe itself. For an early example, an entire teleportation research building is sabotaged to teleport itself deep underground embedded in rocks along with all the researchers inside. And then teleportation became impossible.
- Played for Laughs in The Amazing World of Gumball episode "The Job", where Richard gets a job delivering pizzas. The very concept of Richard being employed is so unnatural that reality starts breaking apart all around him; normalcy is only restored once he gets fired.
- "Time Keeps On Slipping": Stealing chronotrons causes time itself to break apart. Time starts skipping forward at random times, threatening to end the universe itself.
- "Bender's Big Score": Over-use of the Time Code to get away with temporal paradoxes eventually creates the Anomaly, a tear in the fabric of reality. The sequel movie reveals that it's a gateway to another universe where Yivo lives, inaccessible by robots or electrical devices, and what shklee uses to invade the regular universe with via tentacles.