This happened to Hey Arnold! back in 1998: Ep 48, "Arnold's Room", aired September 9, surrounded a Zany Scheme in which Sid takes over the titular room to show off to his rich classmate. Ep 44, "Rich Kid", had introduced said classmate... but aired December 28. The kicker? Those two episodes were the only episodes in which this classmate had a speaking role.
After the first season, production decided to replace Ms. Slovak with Mr. Simmons as the teacher for Arnold's class. Simmons' first appearance was at the start of Season 2, but several episodes produced during Season 1 still hadn't aired by this time, so Ms. Slovak appeared a couple times after being replaced. One leftover Season 1 episode even made it all the way deep into Season 3.
The most puzzling example, however, is airing the sixth episode of the third season as the "season premiere", especially given that the episode had many references to events that occurred earlier in that season. Fans were understandably quite confused.
Danny defeated the Monster of the Week in that episode with a power he got in the season premiere and advice from a character from that very episode.
More egregiously, the fact "Reality Trip" was aired after episodes that it was supposed to precede removed any level of shock about Danny's secret being revealed in the episode; having seen the episodes that took place after it and noting that the status quo was unchanged, it was obvious to everyone ahead of time that a Reset Button would be used.
"The Ultimate Enemy" was aired prior to "The Fenton Menace", despite it being clear by events in the episodes that "The Fenton Menace" had to have occurred first.
The heroes meet Chuckles for the first time in the 13th broadcast episode, "The Way of the Dave", but they also face him in at least three of the episodes that came before it. A number of other scenes also betray the fact "The Way of the Dave" was probably supposed to begin the show.
The 20th episode broadcast introduces Quozmir, who Dave already interacted with in the second episode Disney Channel showed.
Season 1 of Rocko's Modern Life is another example. The fact that Heffer's adopted family are literally wolves is supposed to be a big shock, but their formal introduction to the show aired after they had made a couple of appearances. Likewise, Filburt switches back and forth between being an anonymous Obstructive Bureaucrat and Rocko and Heffer's friend, and Rocko is shown to be already working at Kind-of-a-Lot-O-Comics before the episode where he is hired there.
Rugrats usually doesn't do continuity, but they made a few episodes involving kids from Angelica's pre-school coming to her house... which, in the US, ended up airing long before the episode introducing the pre-school was aired.
The Wild Thornberrys aired an ep about Nigel Thornberry getting knighted in March 2004... after they had aired an ep where a character addresses him as Sir Nigel in February.
Justified for As Told by Ginger when Kathleen Freeman died. Freeman played a teacher, and an episode had one of her students trying to convince her to continue teaching after she'd quit in disgust. Originally, she was supposed to come back to work, but her death forced a rewrite... and the last episode she'd worked on (originally the next after this one) to be shuffled to before.
Nick also held back a season 1 episode of All Grown Up!, which sees Angelica celebrate her 13th birthday, until August 2004... which was also 13 years to the month that the predecessor series debuted. It was held back so long, a few episodes of the following season had already debuted a few months before.
Fox changed the mid-season The Simpsons episode "The Father, the Son, & the Holy Guest Star" to the season finale. Probably justified because the episode made fun of some aspects of Catholicism, and the date it was originally scheduled to air was very close to Pope John Paul II's death, and the change didn't mess with any continuity of the season or series.
The first season had its order screwed with enormously, resulting in Santa's Little Helper not appearing in half the episodes despite being introduced in what ended up as the series premiere (with the intended premiere, "Some Enchanted Evening", airing last).
The major reason for Season 1 becoming all jumbled around was that the episodes entering production prior to "Simpsons Roasting On An Open Fire"note 8th episode in production order but first to air, had such terrible animation that Matt Groening and his team kept sending the episodes back to Korea to be redone.note "Some Enchanted Evening" was remade no fewer than three times... and Matt still wasn't happy with the final result. By the time early episodes reached the point they were "airable", the fall schedule had already been locked in sans Simpsons, so Fox slotted the series in the first available place... which was in late-December. As it happened, there was a Christmas episode ready to go, so it became the premier.
Disney aired its American Dragon Jake Long Halloween episode late to time it near Halloween. This resulted in a character who was imprisoned in a previously-aired (but produced later) episode to apparently suddenly never have been imprisoned yet.
Part of the first season of Thundercats was initially aired out of order; mostly this does not affect much, as the first season is largely in Anachronic Order, but there is a five-parter that is spread over several weeks as a result. Subsequent syndication airings corrected this problem, but the DVD boxed set uses the original, erroneous airing order.
Clerks suffered terribly from this. Episode 4 - the courtroom episode - was shown first, instead of the premiere episode that the network mandated be done in the first place. (On the DVD commentaries, the staff admits they weren't too thrilled with Episode 1 and had some say in the decision, though). The second episode to air was Episode 2, but it was a Clip Show that kept flashing back to Episode 1, which never aired at all.
The second season of W.I.T.C.H. has an insanely frustrating one where they aired the Halloween Episode about four episodes early to be close to Halloween, but the second series was a serial that went almost directly from one episode to the next. There were several characters (re-)introduced, new terms mentioned, and alliances changed (i.e. why were they working with Phobos, why the hell was there a talking cat, what are regents?) and it ruined one of the big surprises near the end of season.
The episode "Tick, Tick, Tick" clearly shows Team Possible's first run-in with Dr. Drakken and Shego, but was originally broadcast after another Drakken-Shego episode ("Crush").
In the first season of Legion of Super Heroes, several episodes made brief references to previous ones, but this bit everyone in the ass with a Continuity Nod in "Brain Drain" mentioning a run-in with magic—from "Child's Play," which hadn't aired yet. After that, the second season avoided them entirely.
Kids' WB! aired Teen Titans episodes out of order. Since Teen Titans wasn't too tight with continuity this wasn't so bad - until the second season, when they aired "Titans Rising", the episode where Terra joins the team, but then aired "Date with Destiny" and "Transformation" afterwards. So basically Terra joins the team and then the next two episodes she's nowhere to be seen, confusing the kids that didn't get Cartoon Network, which aired these episodes in production order, and correctly showed "Transformation" and "Date With Destiny" before "Titans Rising".
The first season of Spider-Man: The Animated Series had several episodes aired out of their intended order, although since the first season didn't have as much continuity as all the later seasons, it wasn't too jarring. Difficulty now is figuring out just what the intended order actually was, since even the production order doesn't make perfect sense.
When the series became more serialized and actually numbered the episodes, it became more noticeable. In Season 2, the "Tablet of Time" and "Ravages of Time" two-parter aired before "Blade, the Vampire Hunter" and "The Immortal Vampire." The latter two-parter resolved the Morbius arc and clarified how Spider-Man's neogenic disease was being treated, while the former two-parter was supposed to lead directly into the season's final two episodes.
In Season 3, "The Spot" was aired before "Venom Returns" and "Carnage" - even though those two episodes set-up the time-dilation technology and Tony Stark's involvement with it. As it aired, viewers wondered why Tony put in a brief appearance in that episode and why he was so concerned about the technology. And like with the Season 2 example, "The Spot" was supposed to set-up the season's concluding two-parter.
Season two of Gargoyles had 52 episodes, making it impossible to tell which would be ready on time. Hence, given the show's very tight continuity, the episodes had to be split into various "blocks" where episodes could be aired in any order within each block. Though they did still run into a problem with Owen's stone arm, as two episodes intended to air before it happened ended up being delayed.
KaBlam! suffered from this a lot. The first episode aired as the twelfth, episodes with cliffhangers aired weeks after the first episode with the storyline was. The season one finale aired as episode ten, the season two premier became the season two finale (you could tell: only season one clips were shown in a flashback sequence, plus it was supposed to start a relationship with Henry and June for the start of the season, plus a character who was introduced in the episode made a cameo in an earlier aired episode (out of order)), the season three finale (and supposed series finale until the show got renewed) was aired as the third episode of season three, and once it was renewed for another season, one mid-season four episode aired as the season four finale (which didn't sit too well with fans - it was poorly-written, and Nick did not renew the show for season five), and the finale for that season aired mid-way.
If you watch Season 8 in production order, you'd notice something odd. In 801, "Good Times With Weapons", Cartman briefly talks about The Passion of the Christ. In 802, "AWESOM-O", Cartman's mom mentions that he's "still supposed to be grounded for trying to exterminate the Jews two weeks ago", likely confusing production order viewers. In episode 803, "Up the Down Steroid", Kyle and Cartman have a serious discussion about the morality of Cartman's plan, which Cartman counters with what The Passion taught him about Jews and Hell. 804, "The Passion of the Jew", is the culmination of what 801 and 803 are building up towards, and the plot involves Cartman trying to exterminate the Jews. So why does the second episode refer to something that doesn't happen for two episodes? Because it was the fifth episode to air in the eighth season, and the show itself has a unique Animation Lead Time.
The season 4 episode "Old Glory" in King of the Hill had a slight continuity error showing Peggy with an old Kaypro computer when the previous episode "Hillennium" had her new iMac arrived. This is because "Old Glory" was produced before "Hillennium".
This happened a lot with The Disney Afternoon shows but wasn't usually a problem, as they're mostly episodic shows.
Then there was Darkwing Duck. As a superhero show, most of its villains and secondary heroes had origin episodes or at least first appearances. Also, Morgana started out as a villain and then did a Heel-Face Turn, even becoming Darkwing's girlfriend. Needless to say, it was hard to keep up sometimes.
Goof Troop was aired out of order on syndicated channels. The series pilot was placed just a little before halfway through the series, which wouldn't have been so bad if it hadn't also been a Welcome Episode. On the flipside for making the third episode first, it's a little strange seeing Pete want to apologize to PJ for doing "nasty, horrible" things when the worst thing we've seen him do is threaten to ground him (admittedly in an over-the-top manner) for failing a test. The pilot episodes establish Pete as unambiguously abusive towards PJ, with the latter unambiguously unhappy about it.
Jane and the Dragon was originally planned to have much more apparent continuity between episodes than most animated shows for kids but was rewritten to be more episodic when the writers were confronted with this eventuality.
During the first season of Justice League, the producers held back the airing of "Injustice For All" eight months, so that it would coincide with the Video Game with the same name. But since it did air elsewhere during that period, it didn't take long for spoilers and pirated copies to appear online.
The episode "Hearth's Warming Eve" is Season 2's 13th episode in production order, but 11th in broadcast order (since it's a Christmas Episode, more or less, and moving it up put it closer to the holiday in question). This bumped the 11th and 12th episodes, "Family Appreciation Day" and "Baby Cakes", to spots 12 and 13, respectively. Fortunately, none of the episodes in question referenced each other (and, considering the nature of the show, could be watched out of BOTH orders without having any negative impact on continuity). Hasbro's website and My Little PonyYouTube channel, The Hub and its website, Google Play, and Netflix all number the episodes in production order; the iTunes Store ordering went back and forth through both styles, but it eventually settled on production(a quick primer) "Hearth's Warming Eve" was initially in slot 13, going with production order - only to be moved to slot 11, airdate order, the very next day. "Family Appreciation Day" was put up also as Episode 11, resulting in two Episode 11s. "Baby Cakes" went up as episode 12 - implying they would later move "Hearth's Warming Eve" back to 13 and go with production order. However, sometime after putting up episode 15, they instead moved "Family Appreciation Day" and "Baby Cakes" to their airdate order slots. Yet it didn't end there; over half a year later, they switched from season-based listings to volume-based listings (seemingly due to the then-recently-added Season 3 consisting of half as many episodes as each of the previous seasons), with the new listings putting the three back in production order. While all this was going on, "The Last Roundup", fourteenth episode in both production and broadcast order, was dropped from the queue completely due to controversy involving a character in the Cold Open, leaving the middle of Season 2 in absolute flux. Confused by all this yet?
The episode "Just for Sidekicks" is Season 3's 8th episode in production order, but 11th in broadcast order (this is because it and the 12th episode, "Games Ponies Play", are Synchronous Episodes). This bumped the 9th, 10th and 11th episodes - "Apple Family Reunion", "Spike at Your Service" and "Keep Calm and Flutter On" - to spots 8, 9 and 10, respectively.
The Italian dub of Season 2 places "A Canterlot Wedding" before "The Return of Harmony", in order to sell Pony Wedding toys which came to Europe four months before the premiere.
Forget about the Italian dub, almost every country seems to broadcast it first to sell toys. Through most of them broadcast it after "The Return of Harmony".
The The Avengers: Earth's Mightiest Heroes episode "Widow's Sting" reportedly takes place after a three-part storyline in which the Avengers stop Kang the Conqueror from taking over 21st century Earth. However, Disney XD aired it before the Avengers even met Kang. Producer Josh Fine says the episode mostly works well in either position, but also that "one minor character point" in the episode "Hail HYDRA!" makes more sense in the chronological order. "Widow's Sting" ends with Nick Fury learning about the Skrulls' invasion, and "Hail HYDRA!" contains a few acknowledgments of his disappearance. Having Kang's invasion come in between those two episodes creates the impression that Fury put off preparing for the arrival of additional Skrulls.
Another point that might deserve mentioning involves the part where Kang says that a disaster during the Kree-Skrull war will destroy the entire world. Iron Man then brings up the fact the Avengers already met the Kree, and know of their imminent arrival. If Disney XD aired these episodes in chronological order, this arc would have come right after the Avengers met Captain Mar-Vell.
The production order of Daria places the slightly-existential "Through a Lens Darkly" as the season three premiere. However, MTV decided to kick things off with the Musical Episode instead. Later, the DVD arranged the third season episodes so that the musical would take up the seventh spot, and "Through a Lens Darkly" could designate the start of the season.
On April Fools Day 2007, [adult swim] aired the final episode of Perfect Hair Forever, but then aired the rest of the series IN REVERSE, made it look like old VHS tapes, and added grammatically incorrect subtitles. At one point, the subtitles shown were actually for an Aqua Teen Hunger Force episode.
The premieres of each Good Vibes episode from Ep. 2 onwards were all aired in the wrong order instead of chronological order. The most notable example being Red Tuxedo, which was the intended season finale, airing as the eighth episode, while Backstage Babs (the ninth episode chronologically) aired as the season finale (and ended up as the series finale too).
Batman Beyond had one that could be seen in the second season. In "Hidden Agenda" Maxine discovers that Terry is Batman, and covers for him by saying she could not babysit for him. The very next episode, "Bloodsport," has Maxine meet Terry at an arcade and is introduced to his little brother for the very first time.
Motorcity suffered from this from the third episode on. While the story was told in an episodic format, focus episodes for each of the Burners were heavily shuffled around, notably prolonging Julie's focus episode (originally episode 6) and a key Chuck episode (episode 8).
The Jimmy Neutron special "The League of Villains" featured villains Baby Eddie and Grandma Taters. This aired before "Clash of the Cousins" and "One of Us", which were supposed to be the introductory episodes for the two.
Season 3 of King of the Hill experienced this. A plot arc throughout the season was Luanne's hair slowly growing back after it was burnt off; Some of the episodes where it's completely grown back are followed by episodes where it's much shorter than usual.
They were much more careful in Season 4, since Debbie doesn't appear in any episodes following her death.
Most of the first season of Moral Orel and some of the second season was aired out of order. The first season's finale was aired first, so that a Christmas episode would air in December, although that initially put new viewers off from the show due to the first season's Downer Ending, making some think it was intentionally humorous, while it was supposed to be out of place with the rest of the season. The last three aired episodes of the first season were ones held back by Standards & Practices, as the final one aired (featuring Black Comedy Rape) was intended to be the second episode. The third season avoids this, partially by featuring a "[Number] out of 13" at the beginning of each episode.
Like some of the above examples, the geniuses that run Cartoon Network have done this with Ben 10: Omniverse, as several episodes have aired showing new things or aliens Ben doesn't have yet. For example "Special Delivery", aired as the season 2 finale, showed Ben with Feedback despite Ben not regaining him until "Showdown Pt.1 & 2", which aired as the third season premiere. That episode also introduced his new Tenn-Speed motorcycle, which Word of God says he doesn't get until "Rules of Engagement", which doesn't air until near the end of the season.
A couple of episodes of Garfield and Friends aired like this during its first season. For example, "Peace and Quiet", "Wanted: Wade", and "Garfield Goes Hawaiian" - the sixth, seventh, and eighth cartoons produced - were aired first, not "Garfield's Moving Experience", "Wade, You're Afraid", and "Good Mousekeeping", the actual first through third cartoons produced. The same goes for Season 7: "Change Of Mind", "Temp Trouble", and "The Perfect Match" and "The Legend Of Johnny Ragweedseed", "Grape Expectations (part 1)", and "Catch As Cats Can't". The latter episode and "A Matter Of Conscience", "Grape Expectations (part 2)", and "Ten Good Reasons" were the first to air that season, to avoid a plot-hole in the U.S. Acres cartoon.
When Nickelodeon aired Danger Mouse, there were two episodes dealing with a time-traveling grandfather clock. The first was "The Hickory Dickory Dock Dilemma" (which had DM and Penfold sent through different periods of time); the second was "The Clock Strikes Back" (a megalomaniacal magician uses it to come to present day London). Nickelodeon aired "The Clock Strikes Back" before "The Hickory Dickory Dock Dilemma."
Also, Nickelodeon ran the serialized stories (series 2 through 4) initially when the series started on the network, and then ten-minute episodes starting with a series 1 episode followed by a series five or six episode. Once the season 1 eps were run, the two episodes comprising a show were from series five and/or six. The serial "Demons Aren't Dull" used scenes from the first series (as part of a subplot in which DM is being humiliated on a testimonial show) and, as noted, was shown before the episodes from where the scenes came.
While Recess didn't have this big of an issue normally, though there are a few episodes that aired out of order. "The Great Jungle Gym Standoff", which aired as episode two (part B), does not have Gus in the episode, making it take place before he moved to town. Gus's first appearance is in episode one part B, "The New Kid". It could be possible that Disney/ABC wanted Gus to be introduced in the first episode, which is why the episodes aired like this.
"Germ Warfare" aired before "Good Ole T.J.", while it should've aired afterwards. At the beginning of the latter episode, Gus mentions that Gretchen is never absent from school, which she was in one part of "Germ Warfare".
Chronologically, the three episodes of the sixth season take place before the events of Recess: School's Out, which served as the Grand Finale, and were also produced before the movie during the fifth season, but hadn't aired as part of it. Though had the movie not have been a success, the episodes wouldn't have aired at all- the show was suppossed to end with the fifth season and movie, but thanks to the movie's success, the show was renewed.
After the first and second seasons had aired, ABC had both season's episodes go out of order for their repeat schedule. Disney Channel only made it worse by re-arranging the individual shorts as well. By 2007, the episodes were back to their original orders.
The Grojband Pilot episode, "Smash Up Terby", was aired as the 8th episode in the US.
Likewise the Canadian episodes go in a different order than here, "Smash Up Terby" is still not the first episode, though.