Overtook the Manga

Mokuba: We appear to be locked on course with a giant ocean fortress directly beneath us!
Yugi: That's weird. I don't remember any of this happening in the manga.

—Yu-Gi-Oh!: The Abridged Series

Many Anime are based on a Manga—the Japanese equivalent to comic books. While simply making the anime into a completely Alternate Continuity is common, especially if the manga has No Ending, more often the anime at least tries to follow the major plot points of the original manga.

If a series is especially popular (and/or marketable), though, its anime version will begin before the manga even ends. Because of medium conventions, it takes longer for events to unfold in manga than it does in anime, the average conversion being roughly 2 manga chapters to make 1 anime episode, and this often means that an anime will simply run out of source material. While some manga series are published weekly (e.g., Shonen Magazine/Sunday/Jump, etc), others are published on a monthly schedule (e.g., Nakayoshi, Shonen Ace). However, most anime are aired weekly, which just makes it worse, especially for manga that have just started. The producers of the anime are then in a fix. They can't just wait for the mangaka to produce more material because they have a broadcast schedule to meet. Japanese shows are almost always broadcast solely as first-run episodes with no reruns. No new episodes is akin to being canceled. This is something that is frequently Lost in Translation outside of Japan, since unlike Western shows, they don't schedule production in the form of "seasons" with production breaks set into the schedule. They just keep going and going and going or stop at a predesignated point. This is also why lots of anime are only 12 or 24 episodes long, because that's all they were scheduled for, regardless of popularity.

Unless they work in very close tandem with the writer of the original manga, which is very rare since they're usually really busy with the manga as it is, so the people in charge of the anime will thus have to start making things up on their own, and create a unique plotline from the point they ran out of manga to base things on.

Unfortunately, unpopular or unwelcome filler arcs or filler episodes may often be Misblamed as being the fault of the author(s), when in reality, they may often not have a whole lot to do with the filler plot. Some fillers that were better received by fans are often cited as being opportunities to develop lesser characters. (This often helps with anime that have a cast size near the size of the production staff.)

Another option could easily be to just pad the episodes out and slow the story down. This was common in the Dragon Ball series, which unfortunately caused many people to believe the manga was exactly the same or that Akira Toriyama's writing was at fault; when the pace of the anime was out of his hands.

Most writers just choose to do a Gecko Ending instead.

Film

The Jurassic Park novel series ended with The Lost World, so the movie Jurassic Park III was created from whole cloth. Following the Author Existence Failure of Michael Crichton, this will remain the case for any future film sequels.

Literature

Some of the early Star Wars Expanded Universe material that was published between the movies of the original trilogy, notably Splinter of the Minds Eye. It was written as a sequel to the first movie, but published when it was unknown if The Empire Strikes Back was ever going to be made. The Marvel Star Wars comic book series fits this trope to a tee despite ironically being a comic book adaptation of a screen franchise. First it adapts the first movie, then it has a bunch of original stories, then it adapts the second movie, followed by more original stories, then the third movie, and then it Overtook the Series.
S.D. Perry wrote a follow-up to her Resident Evil 2 novelization titled Resident Evil: Underworld, in which Sherry Birkin is left under the care of her heretofore unseen aunt, while Leon and Claire go on a new adventure with Rebecca Chambers and the surviving members of the Exeter branch of S.T.A.R.S. However, this book proved to be hard to reconcile when Resident Evil 3: Nemesis came out, as it revealed the fates of various characters after 2, which differed to what Perry came up with in Underworld. Perry had to explain away all the continuity snarls in her Nemesis and Code: Veronica novelizations.

Live-Action TV

All Creatures Great and Small: the show eventually ran out of James Herriot novels to adapt and started creating the scripts out of whole cloth.
The Showtime series Dexter had its first season based on the first Dexter book, Darkly Dreaming Dexter. The second season showed an original storyline as the second book, Dearly Devoted Dexter, was considered inappropriately dark for the show. There were no more books by the time the third season was greenlit, and since then the novels and TV series have gone their separate ways.
HBO's Game of Thrones series has one season every year. It's based on George R. R. Martin's A Song of Ice and Fire books, which provide enough material for one season each, possibly two if the screenwriters stretch it, but come out roughly once every five years or more. David Christopher Bell of Cracked.com calls this one of 4 Behind-the-Scenes Problems That May Kill 'Game of Thrones', and he suggests that the series may end up slipping into an Alternate Continuity. But after the first season of this slippage had aired, Felix Clay called it one of 4 Badass Works Of Art That Shouldn't Exist.

Video Games

The Tim Burton Batman movie was adapted to an NES game by Sunsoft, who took great liberties with the plot of the movie but still managed to churn out a pretty good sidescroller. However, Sunsoft couldn't wait for the next movie to come out before making a sequel to the NES game, and created Batman: Return of the Joker by themselves.
A similar example occurs with the SNES adaptation of Jurassic Park. Ocean couldn't wait for the sequel (or even the novel it would be loosely based on) and created their own, Jurassic Park 2: The Chaos Continues. It had a vaguely similar plot to the eventual sequel; a rival genetics company tries to take control of the island by force, and Alan Grant is sent to stop them. Nobody stopped to question why Grant was suddenly a gun-toting Contra-esque mercenary... or why he'd care about any of this. Good music, though.
Street Fighter was another interesting example in that Tiertex, the company responsible for porting the original Street Fighter to home computers (who also did a terrible job at at it) decided they couldn't wait for Street Fighter II to revolutionize the fighting game genre, so they took their port of Street Fighter and made their own original sequel to it, titled Human Killing Machine (which was also quite crap).
Years before Capcom released Strider 2, the official arcade sequel to the original Strider, they handed the Strider license to U.S. Gold and Tiertex (the companies that produced the European computer ports of the first arcade game) to produce their own sequel titled Strider II (spelled with a Roman numeral). This sequel was originally made for the same set of European computer formats and then remade for the Sega Genesis and Game Gear, getting a stateside release in the form of Journey from Darkness: Strider Returns.
When Konami wanted to make a sequel to Metal Gear following the success of the NES port in North America, they commissioned one of their teams to make a sequel specifically for the American market, resulting in the creation of Snake's Revenge. This inspired Kojima to make his own sequel for the MSX2, Metal Gear 2: Solid Snake. Snake's Revenge is not considered part of the official Metal Gear continuity, as the events of the game are incompatible with what occurs in the "official" sequel. Namely, the way Big Boss' return is handle in both games. Both games takes place three/four years after the original Metal Gear and have Big Boss forming a new terrorist organization with a new Metal Gear prototype in his hands. However, in Snake's Revenge he also turns in a huge cyborg during the final battle.
A sequel to the original Gradius (aka Nemesis) was made for the MSX titled Gradius 2 (aka Nemesis II) before the actual arcade sequel, Gradius II (aka Vulcan Venture), was even made.
Golden Axe II for the Sega Genesis was made a year before the proper arcade sequel (Golden Axe: Revenge of the Death Adder) was released.

Western Animation

The Secret of NIMH actually overtook the source material. While the Bluth film was rather jumping in and out of In Name Only, the ending (And primary events) of Bluth's 1982 Animated Adaptation pretty much ruined any potential chance of covering the two books written by Jane Leslie Conly with Jenner and Nicodemus kicking the bucket. (Whereas they both survived in the books; however it was implied that Jenner possibly died off-screen sometime in the first book with the mention of his party being electrocuted by a car battery). But Bluth honestly deserves this... his film was copyright 1982; Conly's books are dated 1986 and 1990, Chances are nobody even knew that Conly would take over or that the official book sequel would be released four years later. (Whether or not the supposed remake will follow the books more faithfully is unknown)
- Bluth has also stated that if he were to make a sequel to Secret of NIMH, he'd actually cast Martin as the hero while Timothy was the villain. Interestingly, the sequel made 17 years later actually did the opposite.
He-Man and the Masters of the Universe: the series was put into production before the comic it was based on (and, by extent, the mini-comics that came with the action figures) could establish a concrete plot. This resulted in the story being retconned to fit in with the show.

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