Example of the "Big Bad manipulates the actors to fight and eliminate each other" trope: the miniseries Crisis on Infinite Earths featured a subsidiary story arc involving Brainiac and the Earth-One Lex Luthor assembling an army of supervillains to attack the remaining superheroes. Brainiac and Luthor had led their villain army to believe that the superheroes would be easily defeated owing to the villains outnumbering the heroes (who were already distracted dealing with the huge honkin' crisis that was unfolding in the main story arc); however, the real plan was to have the heroes and the other villains kill each other off so that when the the dust finally cleared, Brainiac and Luthor would be the last superpowered "men" standing, and therefore be able to take over all the remaining universes without anyone left to defeat them. If Whatever Happened to the Man of Tomorrow? is any indication, Brainiac planned to dispose of Luthor soon after.
In Gotham City Garage, Batman makes Barbara Gordon believe Kara killed their father to turn her against her little sister. His deceit almost works, but Harley tells Barbara the truth before she meets Kara.
In an interesting inversion, Plastic Man #4 has the titular hero spreading himself thin, then standing between two robots, causing them to punch each other through the sheet of his body.
Plastic Man: Hey, hey! Rock 'em Sock 'em robots! Now that's more like it! Let's you and him fight!
During John Byrne's run, Darkseid tried to use illusions to convince Superman that he was battling his minion Amazing Grace and Wonder Woman that she was fighting Kalibak, when in reality Superman and Wonder Woman were fighting each other. Subverted in that the two heroes saw through the deception almost immediately and staged a mock battle, fighting their way toward Darkseid's throne room. As Superman reminded Darkseid, "We may be mere mortals, but we're not stupid!"
This plays out oddly in one issue of Action Comics, where Superman gets into a fight with Diode the Invincible over a misunderstanding... but while he wasn't a member of the murderous Doomslayers roving the area, Diode was a supervillain. After clearing the air, the aged wash-up decided to help Superman take care of the Doomslayers before retiring peacefully.
The series Birds of Prey once hung a lampshade on the trope with a novice crime fighter who was styling herself as the new Batgirl. Using her teleporting powers she had been watching the heroes for a long time and knew not only that they were good guys, but also their names, secret identities and powers, and when they set up an ambush one evening to try and find out who has been masquerading as Batgirl (Something Oracle, the original Batgirl, does not take lightly) she could not have been happier. As they are fighting she happily converses with all the participants and explains that after they are done fighting they can all be good friends and teammates, because she had gained the impression that fighting at the first meeting was the traditional thing to do.
Batgirl (2000) has a brief scuffle between Cassandra Cain and Connor Hawke. Connor comes to Gotham on the trail of bow-wielding assassins, only for Cassandra to assume he's one of them. It ends when Cassandra fakes being knocked out so she can eavesdrop on him and Eddie Myers, confirming they're not the killers.
Discussed in an issue of The Flash where he and the Pied Piper almost come to blows while investigating the murders of some homeless people.
Young Boy: This is gonna be neat! Flash: Neat? Pied Piper: Neat?! Boy: Sure. You guys are gonna fight now, right? On account of you really like each other, but a supervillain made you misunderstand so now you gotta fight. So you're gonna fight for about an hour, then realize that you've got a common enemy and be life-long friends. Pretty neat! Flash: ... Boy, do I feel predictable. Piper: Let's cut to the part where we team up, okay?
Lampshaded in an issue of Justice League of America in the early nineties. Obsidian and Nuklon are waiting to meet up with the JLA to offer to join the team after its most recent roster overhaul, and Obsidian says, "First, they won't even let us join. 'You were in Infinity, Inc.? Wasn't that some kids' group, like Menudo?' Then there'll be some bizarre misunderstanding, and they'll think we're villains, and there'll be a fight, and..."
Batman: No Man's Land has an amusing aversion. Bane manipulates several of the various Gotham gangs into thinking Two-Face has murdered several of their compatriots. Two of the gangs, the Street Demonz and the Eightballs, run into each other while out for revenge and immediately team up to stage an assault on Two-Face's headquarters. No argument, no tension, no Mexican Standoff, no nothing. Apparently, common street gangs are better at teamwork than most crime fighters in the DCU.
In his first meeting with the Legion, the clone Superboy mistakes them for villains. If you translate the Interlac, Saturn Girl says "This must be the 20th century tradition of fighting then teaming-up I've heard about."
The JLA/JSA/Legion teamup in the Lightning Saga subverted this slightly by having Superman introduce the Legion team when they showed up in the past though Karate Kid had been beaten up as Trident earlier and in fact Star Boy had already been on one of the teams. But then they all had issues with each other later.
Also subverted in a different meeting of Superboy and a Legion team. Turns out the mission team had been pretending to be average citizens and had insinuated themselves into his life beforehand.
This was given a possible callback in DC One Million; the Batman of the future (no, not thatBatman of the Future) meets modern Nightwing, and fights him. Nightwing asks why, and Batman 1-mil says he's honoring the superhero tradition of fighting before teaming up.
Blue Beetle and Green Lantern Guy Gardner had one when they first met, as his ring detected Jaime's Reach technology as a threat. Also notable for the rematch having been broken up by one fighter's mother.
In an early storyline of Justice League International, Maxwell Lord and his computer ally sicced the League on Metron after framing him for creating a rampaging robot. Their plan went awry when it turned out that Metron and Mister Miracle knew each other as New Gods and were more inclined to talk things out.
The New 52 puts together the Justice League in this fashion. Green Lantern gets a tip about alien technology in Gotham and finds Batman. They only argue before teaming up, but since the only alien they know of is Superman, they head to Metropolis to question him. GL calls in the Flash when that doesn't go so well, and they all whale on each other for a while until the alien tech activates and starts spewing Darkseid's Parademons.
In New Krypton storyline, Reactron kills Supergirl's father and later frames her best friend Thara Ak-Var (Flamebird) for his murder. In The Hunt for Reactron storyline, both friends come to blows.
In the New 52 story arc Last Daughter of Krypton, when Supergirl arrives on Earth, Superman introduces himself as Kal-El. She attacks him, thinking that he is a villain pretending to be a Kryptonian because she is unaware that Krypton has been destroyed and thinks that it has only been a short time since she left, and when she left, her cousin Kal-El was a mere baby. She eventually relents after the initial misunderstanding.
In The Multiversity #1, the Multiversity team and the Retaliators come to blows after a bewildered Thunderer knocks out his Earth-8 counterpart.
Watchmen refers to a fight between the Comedian and Ozymandias when they first bumped into each other. Ozymandias shrugs it off as a common enough misunderstanding in reference to the trope, but given the Comedian's personality (and the fact that Ozymandias was investigating the disappearance of Hooded Justice, whom the Comedian might well have murdered) it likely wasn't an accident. And while Ozymandias trivializes the incident, the severe beating he administers (or has administered) to the Comedian as part of murdering him demonstrates that he probably wasn't sincere.
Spider-Man's second comic appearance ever (after his Origin Story) was a misunderstanding with the Fantastic Four, who were almost the only other superheroes in Marvel Comics at the time.
As might be expected, Peter Parker from the mainstream universe picks a fight with Miles Morales because he doesn't trust anyone in a Spidey suit. Miles fights him off, however, because only a freaked out and off his game Spider-Man would ever pick a fight with a thirteen year old boy. And mostly because Miles can instantly incapacitate anyone by touch.
Subverted and lampshaded in Peter David's Spider-Man 2099 Meets Spider-Man one-shot. Due to some time-traveling experiments, Peter Parker (Spider-Man c. 1995) and Miguel O'Hara (Spider-Man 2099) switch places. After some running around, the two meet while pursuing a time-traveling Hobgoblin from 2211. Peter Parker/Spidey 1995 promptly quips "I know this is the part where we're supposed to be confused about each other, get into a fight, then settle our differences and chase the bad guy — but we're short on time, so let's just skip all that, okay?" Miguel, dumbfounded, simply agrees.
Lampshaded in The Spectacular Spiderman #13 where, before teaming up, Razorback attacks Spiderman because "Isn't that what superheroes do when they first meet?"
When Spider-Man met Daredevil for the very second time, the Masked Marauder deliberately engineered it so they would come to blows. He did this by having guys in Daredevil costumes taunt Spidey until he hunted down the real one. Why, you ask? So the only two threats to his plans would be too tied up dealing with each other to stop him.
It happens the very first time the two meet as well, thanks to C-list supervillain the Ringmaster hypnotizing Spidey into fighting Daredevil when he's trying to stop him.
In the early years of his solo book, Peter's jerkassery tends to get dialed up a few notches whenever other heroes show up in his mag, even if they did nothing to antagonize him. To an extent, this was an Enforced Trope; any peaceful meeting would probably end with him joining The Avengers or the Fantastic Four, in which case money and/or publicity worries (the bread and butter of the typical Spider-Man comic) would go right down the drain.
Namor the Sub-Mariner decided to take revenge on the surface world, starting with the city of New York. The Human Torch arrived to stop him and the Marvel Universe was born. They later teamed up with Captain America when it was revealed the Axis was the true enemy, a plot Marvel still homages to this day.
The original Avengers team was actually created that way: their members met when Loki attempted to trick Thor and Hulk into fighting each other and accidentally brought Iron Man, Ant-Man and The Wasp into the fight as well. Thor ended up finding out the truth, and the five heroes, after defeating Loki, decided to keep teaming up together.
Lampshaded when, about ten or twelve years ago in real time, The Avengers (actually, robot impostors) arrived in Germany to claim jurisdiction over the Red Skull and take him away in the middle of his trial by the German government. Hauptmann Deutschland wondered if protocol required that he should fight Captain America.
It was lampshaded just a few years into the original book, when (during their first crossover with the X-Men) Hawkeye, Goliath, and Black Panther deliberately staged a clash-of-egos with each other to throw Magneto off-guard. Of course, the fact they expected Magneto (not to mention the readers) to swallow this without question is telling in itself...
Some titles like Incredible Hulk can usually pull these off repeatedly due to his unstable mental nature. One day he's a giant with the mind of Bruce Banner, the next an unthinking ball of green rage. Getting these fights to stop usually involves a Cool Down Hug and the inevitable Hulk's Cooldown Hug Corollary to avoid a change in the Status Quo.
Lampshaded in one instance by Hulk himself. Granted he was in the middle of his "smart Hulk" phase, but during the Marvel Knights sagas he runs into Ghost Rider. Unfortunately for him, fortunately for the reader, Ghost Rider is in screaming Spirit of Vengeance mode, and he's not having any of it.
Hulk: Alright, I get it. This is the obligatory "good guy meets good guy, they have an obligatory fight based on misunderstanding, then team up to fight the REAL bad guy. Can we just skip it?"
Sleepwalker's lack of understanding about the human world and its heroes led him to end up fighting with Spider-Man, Deathlok and Ghost Rider at different points in his short-lived series. Thankfully, both of the comic's regular readers were spared Wolverine and The Punisher guest starring.
Used twice in Marvel 1602. Peter Parquagh is sent by Sir Nicholas Fury to deliver a message to Carlos Javier. Before he can even reach the gate, Hal McCoy pins him to the ground and accuses him of being a spy. Earlier, Parquagh is sent to bring Virginia Dare to visit the queen and is waylaid by her bodyguard Rojhaz. Rojhaz (who later turns out to be Steven "Captain America" Rogers) protests his exclusion from the meeting by lifting Peter up by his shirt.
Subverted in Spider-Girl, when she runs into Araña (Grown up version of the 616 Araña, who currently is the mainstream Spider-Girl, to boot), who wants to fight her. May absolutely refuses, since she refuses to turn "the hero biz" into some sort of "who's stronger" contest and runs away. But Araña chases her and goads her into fighting. From the start of the sequence:
May: I don't do "tests", "misunderstanding battles", or "grudge matches".
Deadpool once explained the real reason heroes do this: It's fun.
Citizen V: This fight is completely unnecessary. Deadpool: BLASPHEMY! All fights are necessary!
In the Soviet Super Soldiers oneshot, the Crimson Dynamo laments that "a prerequisite to every visit I make to the United States seems to be a completely gratuitous battle against people I don't even know."
Black Panther in his first appearance in Fantastic Four attacks the Four to prove his worthiness to defend his kingdom and the usefulness of the team to help him. After making that point, he stops the fight to explain himself to the team and makes it up to them for the incident.
Happens between the Avengers Academy Students and The Avengers in Issue #21 then again between the students and the X-Men in the next issue! Previously, they also got in a fight with the Runaways, because of Hank Pym, in yet another one of his asshole moments, had plotted to kidnap Molly Hayes and Klara Prast. Thankfully, most of the Academy's students realized it was an asshole plan.
Most of the team versus Cloak & Dagger, who think they're criminals holding Molly hostage. Alex tries to point out how old the routine is, but the more experienced heroes make short work of them. (According to Dagger, Stilt-Man took longer to beat - ouch.)
The Runaways also ended up fighting Joss Whedon's Astonishing X-Men over a misunderstanding. While the two teams traded blows, Kitty Pryde and Gert sat it out and ended up resolving the issue over a nice conversation.
Somewhat lampshaded in a Marvel Team-Up miniseries a few years back. Wolverine is searching for a potentially dangerous teen mutant that happens to be talking with Spider-Man. When Wolverine attacks Spider-man, he dodges the berserking attacks and asks why do they keep having to fight every time they meet.
This is a very popular device across the various incarnations of the Marvel Team-Up series, often with slight justifications; In Marvel Two-In-One #15, the Thing and Morbius are constantly coming to blows because the Living Vampire is trying to slake his thirst throughout the issue — to the point that they all but ignore the villain of the piece.
Justice Peace and Thor in The Mighty Thor #371. This one has consequences: the fight delays Justice Peace's pursuit of the serial killer Zaniac, who kills several more people before they catch up with him.
Avengers vs. X-Men not only pit the two groups against each other, it had its own tie-in miniseries dedicated to just the hero vs hero fighting (AvX VS)! Mind you, in this case there isn't any misunderstanding or mistake in identity involved - the two teams simply want things that are mutually exclusive. But some fans feel that the speed at which they resort to violence is just as contrived.
A variation in Avengers Arena, in which Arcade kidnaps a number of young mutants and heroes and forces them to fight each other for his amusement in a parody/Shout-Out to Battle Royale. The involved heroes are even aware of his plot right from the start and most of them actively try not to play it straight because they do not want to play Arcade's game and try not to kill anyone. Sadly, fights still happen because of misunderstandings.
Nova: Both played straight and lampshaded in one issue of vol 4., when Richard and his old teammate Darkhawk fight. Darkhawk refuses to listen to Rich, on account of there being a Skrull invasion going on, having already been attacked by Skrulls disguised as other heroes. Not helping is that the source of Darkhawk's powers make him unreasonable and angry at the best of times anyway. However, Rich's little brother intervenes and determines Richard is who he says he is, before shortly mocking this trope.
Robert Rider: Isn't it traditional for super-heroes to fight before realising they're on the same side? Darkhawk: (To Nova) Did you want to hit him a lot when you were a kid, too? Nova: All the freaking time.
X-Men 2099 featured the odd case of a "first-meeting misunderstanding" fight that had a lasting effect on the plot, occurring during the X-Men's first encounter with the similar group Freakshow. X-Man Metalhead was assaulted by Freakshow member Contagion, whose touch spreads a deadly disease; Metalhead survived because he was in metal form, but his body was mutated and he lost the ability to turn his powers off. Ashamed of his new monstrous appearance, he joins Freakshow (seemingly with no ill will towards Contagion) and doesn't appear again for a while.
A spectacular pile-up of this trope occurred in the Ultimate Spider-Man comic. Peter heads out to stop an up-and-coming crime boss named The Kangaroo only to find Daredevil's already there for the same reason. Daredevil then promptly drops what he's doing to beat the crap out of Peter really for no reason other than believing a teenager is too young to be a super-hero. This is soon dropped when The Punisher arrives, also to stop (read: kill) the Kangaroo and begins riddling the building they're in with bullets. Then when Spider-Man and Daredevil are trying to stop him (while still butting heads and insulting each other) Moon Knight shows up and only adds to the fighting. The Kangaroo attempts to skulk away unnoticed during all the fighting but Daredevil slips away long enough to apprehend him.
Team Leader 1: "Everybody on the alert, this may be a hackneyed plot contrievance!"
The Punisher gets this all the time, in part due to the fact that many heroes see him as a legitimate threat (they want to arrest criminals, he wants to kill them).
Several stories have Daredevil or Spider-Man show up to stop Frank. Depending on whose series it is, he either incapacitates them long enough to shoot whatever mobster he was there to kill, or incapacitates them long enough to run away.
In the "Blood And Glory" story, he's even manipulated into shooting Captain America by a corrupt Attorney General (who makes him out to be behind the US selling deliberately faulty weapons to a South American dictatorship).
One Daredevil / Punisher crossover sees Frank and Matt believe each other to be working for the criminals due to Frank murdering an attorney Matt was friends with. Matt later learns was Frank was correct and the attorney had been taking bribes.
One story has both the Punisher and Wolverine hunting the same poachers. Naturally, Wolverine sees Frank with a gun near a bullet-riddled dinosaur and goes for him. They only stop when they realize on of the expedition's guides is aiming at them, encouraged by the leader's wife.
In a later story, the Punisher and Wolverine are after some bizarre mob kidnappings (and it's not Frank this time). The victims are found with their legs cut off (Wolverine thinks Frank is the kind of sick bastard to do this, Frank thinks Wolverine's claws were used). It turns out a mob of Depraved Dwarves was behind it, and believed the two would join them (Frank because he kills criminals, Wolverine because he's short too).
Secret Empire deconstructs this trope along with Teeth-Clenched Teamwork. By the time of the crossover, the heroes have spent so much time fighting each other that there's no sense of trust between them. Not only does the evil Cap take advantage of it to easily get the heroes out of his way, Ultron, who has spent his whole existence trying to wipe out mankind, ends up deciding to just kick back and wait for the superheroes to do it for him because all their conflicts have done a darn good job breaking everything.
When the Imperials raid her auction, Aphra ultimately leads a group of Stormtroopers into a room full of criminals who all want to kill her for a variety of other reasons, letting them all shoot at each other. Later, she also leads the rampaging Rur crystal-powered droid into the room as Darth Vader arrives, letting them fight.
When captured on Milvayne by Tam Polsa and a squad of local law enforcement, and facing execution, Aphra points out that Polsa is a vigilante. As she hoped, this causes the squad to deem him a renegade and turn on him, creating a distraction that lets her escape.
In the Kurt Busiek/George Perez crossover miniseries JLA/Avengers, in which the two title teams were pitted against each other in such a gambit — but after the initial encounter, Batman and Captain America (realizing they were being played) removed themselves from the ongoing contest to figure out why. Which was seriously the moment you knew the bad guys had lost. Bats and Cap, working together? You're screwed, Krona.
But in the third issue, Cap holds on to the Conflict Ball pretty tight, as well as Superman (because they are both deeply synced with their universes' natural vibrations), as seen in one of the 80s League/Avengers meetings, in the Avengers Mansion: Cap freaks out and starts yelling at Supes, causing them to clash with each other and reality to shift again. Just moments later, as they are about to throw down again, Wonder Woman and Wasp break up the fight and make them realize they should be cooperating instead of wasting time butting heads.
In the first Spider-Man/Batman, it's averted in that Spider-Man turns out of be a huge Bat-fanboy, winning Batman over with sheer persistence; the only resemblance of a fight was a punch by Batman and a Judo Throw by Spidey. By the second crossover, they basically shake hands and agree to team up, with Spider-Man pointing out to a resistant Batman that they went through all of this the first time; they could either waste time fighting between themselves and approaching the case from different angles, or they could pool their resources from the start and work together. After a moment, Batman conceded the point. A humorous scene from this very same team up showcased Batman's true feelings on it. When they were both in the Batmobile and Spidey was riffing on something or another about how cool the car was, Batman grumbled that he now understood why Superman worked alone.
Early on in The Savage Dragon, Badrock from Youngblood randomly appears and attacks Dragon. They cause a bit of property damage, then Dragon gets the upper hand and Badrock begs off. He says he was just testing to see if Dragon, who had just recently appeared and joined the police force, was tough enough; that kind of thing "happens all the time in Marvel Comics." An incredibly pissed off Dragon proceeds to arrest him. Note that Badrock is a mutated grade schooler so he really wouldn't know any better.
Badrock also provoked a fight on accident when Freak Force took in a villain he fought and were going to claim the reward money. And then he hit on Ricochet and in general acted like an idiot. All told, both sides were justified in wanting to beat the other up.
Another incident happened when Dragon was sent to Hell and ended up alongside Spawn, who was trapped there for his own reasons. When the Fiend tried to force Spawn to fight Dragon to escape that level, Dragon, whom was still convinced he was dreaming at the time, promptly threw the fight, allowing Spawn to go on.
When Daredevil is tracking down clues in some sewers, Batman almost gets the drop on him, thinking he's the culprit. You'd think a guy who dresses up like a bat wouldn't be so judgmental about a guy who dresses up a devil. Both act Out of Character throughout the crossover.
As mentioned in Linkara's review, this was surprisingly averted in the Care Bears / Mad Balls crossover comic. There's an obvious set-up for it, but the protagonists manage to avert it by not being complete idiots.
In fan and critical fave crossover X-Men / New Teen Titans, there's no conflict between the teams at all (thanks to Prof X). Instead, the time is better spent exploring how the superheroes would react to each other on a personal level. For instance, Starfire hears Colossus speaking Russian, and immediately gives him a long passionate kiss (since that is how she can instantly learn a new language) - which makes Kitty Pride jealous. Nightcrawler humorous asks, "Hmmm... Fraulien, sprechen sie Deutch?"
Averted in the "Shades of Green" arc from Usagi Yojimbo. A wizard summons the Teenage Mutant Ninja Turtles to the past to help Usagi and Jen defend his village from evil ninjas. The turtles take defensive positions and are about to attack Usagi and Jen when Leonardo (who met Usagi in an earlier story) says, "Wait a minute, I recognize that guy!" He and Usagi exchange pleasantries and Leo's brothers decide that if he trusts Usagi they will trust him as well.
The Justice League/Mighty Morphin' Power Rangers crossover starts out with this. Zack gets teleported to the DC universe mid-battle and lands right in front of Batman. Concussed and disoriented, he assumes Batman's another of Lord Zedd's monsters and attacks. Then the other Rangers arrive, see Batman fighting their teammate, and promptly jump in. Batman calls the Flash for backup, and things escalate from there, with the Dinozords coming out before things get smoothed over.
Super Sonic Special: Battle Royal was all about this trope. Basically, Mammoth Mogul attempted to turn the Freedom Fighters and the Chaotix against each other by using his powers to disguise his private enforcers, the Fearsome Four, into the other members of the two teams. Unfortunately for him, both sides are able to spot key flaws in the ruse, secretly compare notes, and fake a mutual destruction in order to draw Mogul out.
In Sonic the Hedgehog/Mega Man: Worlds Collide, the first act of the crossover is dedicated to setting up an epic brawl between Sonic and Mega Man. It gets lampshaded in Mega Man #24's "Short Circuits" segment, where both title characters are eager to work together before being informed by Orbot that they have to follow the "crossover by-laws" and fight each other first.
Happens in one Astro City story between Samaritan and The Confessor, though The Confessor knows the fight is pointless because he knows there's a misunderstanding involved. But he goes through with the fight anyway because he can't allow the ultra-powerful hero to push him around.
This trope is also played for drama in the story "Sorrowsday". Krigari Ironhand, a dimensional conquerer, is goaded by a mysterious stranger into attacking the super-team Honor Guard. The two clash repeatedly over the years until Krigari is finally defeated thanks to a Heroic Sacrifice by guard member Stormhawk. The stranger is then revealed to be Eth, an alien who was trying to stop Krigari before he could conquer Eth's realm — and becomes racked with guilt over causing Stormhawk's death.
Defied in Aztek: The Ultimate Man. When Aztek is confronted by an angry Green Lantern out for a fight, he simply swipes Kyle's Ring of Power and then hands it straight back.
Aztek: Good, well, now that we've passed the predictable fight superheroes are obliged to have when they first meet and established the fact that I'm not a villain, maybe we can get down to business here. Friends? Kyle: Ring first, then friends.
Subverted in the backstory to the comic book miniseries Common Grounds: two superheroes, an experienced one and a novice, accidentally fight each other (a situation referred to by one character as a "knuckleduster"), and the experienced superhero kills the younger one. The survivor is subsequently arrested, sentenced to a lengthy term in jail, and emerges decades later unable to find gainful employment, forced to scrounge through the trash for meals. This actually serves as the key background moment of the entire series, as it was this event that lead to the foundation of the titular series of restaurants. The founder of Common Grounds, himself a former hero, was the father of the inexperienced hero killed in the brawl, and he started the neutral-ground eatery as a means of insuring that heroes (and even villains) would finally have a chance to meet one another and be able to clear up these minor confrontations before they could spin out of control in the real world.
Lampshaded in the Doctor Thirteen limited series. At one point, Infectious Lass asks if there's going to be a superhero fight, and then points out that in the 31st century, it's common knowledge that superheroes are supposed to fight each other before teaming up.
The first two issues of Gen-Active are about Gen¹³ running into some of their old archenemies, the Deviants. However, the Deviants are reformed at this point and, for the first time, don't want to kill Gen 13. Fights break out, though, because Gen 13 members make assumptions and start something. It keeps happening because neither side is willing to just talk to the other after the fight's over.
In normalman, Captain Everything and Sgt. Fluffy have a pointless fight the first time they meet in the series... despite the fact that even Dumb Muscle Cap is aware that they're on the same side and have known each other for years; it's just something that you do.
Subverted in Paperinik New Adventures:the first time Xadhoom met Paperinik, she saved him from a group of Evronians,so he went to thank her, and she tries to kill him too, thinking he was an Evronian. It was played straight during his first encounter with Urk, but is more justified because Paperinik has some proof that he was the mysterious kidnapper who was terrifying Duckburg, and Urk had no idea who he was.
Subverted in a Radioactive Man story - Radioactive Man and Bleeding Heart are trying to track down a cult that has (apparently) abducted Fallout Boy. Along the way, they encounter a hippie superwoman called Black Partridge, who attacks them for the cliffhanger. When part 2 opens, the men explain that traditionally they would misunderstand each other, then fight, then finally realise they're on the same side and team up against the common enemy, only they're in a hurry at the moment so could they skip the fighting part?
Sonic the Hedgehog (IDW): Issue #6 sees a fight between Sonic and Shadow break out due to their disagreement over how to handle the amnesiac Eggman. It turns out that Rouge engineered the events leading to this fight, figuring a brawl with Sonic would clear Shadow's head enough that he wouldn't outright murder the Doc.
Played frustratingly straight in Marvel UK's Transformers story "Time Wars". A group of Autobots from the future come back to help fight Galvatron...and the present day Autobots attack them on sight, resulting in an issue long fight sequence. The thing that raises it to ridiculous proportions is that the present day counterparts of at least two of the future Autobots were part of the present day line-up at the time...yet none of the present day Autobots recognise them.
Happens in issue #12 of Strikeforce: Morituri, with a fight between the current Morituri team and the third-generation recruits.