Mistaken for Aliens

When characters are mistaken for the beings of another world. If you travel through time (especially to the mid-20th century or thereabouts) or are an astronaut, this will probably happen to you at least once.

Yet another variant of Comedy of Errors.

Examples of Mistaken for Aliens include:

Anime and Manga

Rena from Higurashi no Naku Koro ni mistook her friends for aliens in "The Atonement" chapter. Of course, she was at best, at lv.4 Hinamizawa Syndrome
One episode of Ouran High School Host Club had Honey's younger brother Yasuchika accuse him of being an alien simply because he eats three cakes at once in less than a second once a week.
Franken Fran helps an actress who has fallen for a male lead who is obsessed with anime features, and wants to star opposite him in live-action adaptations. She insists on ever more extensive surgery but fails to take Fran's advice at the hazards in her rush to bed the actor, and cosmetically falls to pieces. He flees in terror, then goes on so many talk shows raving about Grays trying to abduct him that he doesn't get any more roles.
A running gag in Squid Girl - Cindy Campbell and her colleagues are convinced that Squid Girl is from outer space, and they would very much like her to visit their laboratory.

Comic Books

The Teenage Mutant Ninja Turtles Mirage do this on purpose in the third Mirage comics volume; aliens having openly made contact with Earth, it's apparently easier for people to accept that than homemade mutant freaks.

Film

Midway in the Super Mario Bros movie, our heroes are labeled as aliens when they escape from Koopa.

Luigi: Aliens? Now we gotta deal with aliens too?
Mario: Luigi, we're the aliens!
Luigi: We are? Cool!

In Back to The Future, the DeLorean Time Machine was mistaken for a UFO in 1955 due to its gull-wing doors. The fact that Marty was wearing a radiation suit at the time didn't help.
- He turns it to his advantage later, when he orders his father to hook up with his mother.
Grand Fenwick's chainmail-clad longbowmen successfully invade 1950s New York City in The Mouse That Roared because of being mistaken for Martians.

Literature

In Spider Robinson's The Free Lunch, when the protagonists notice that there's something very odd about some of the attendees at the theme park where they live, their initial deduction is aliens. This being Spider Robinson, however, they're actually time travellers.
Take Me to Your President by Leonard Wibberley was about a fellow nicknamed "A-1" from a small British town called Mars, who accidentally got loaded into an experimental rocket. When it landed somewhere other than it was expected to, and he came out wearing the space suit he'd found and saying he was from Mars, well....
In Amy Thomson's The Color Of Distance has the protagonist, Dr. Juna Saari, spend five years among the alien Tendu, who give her a moist color-changing skin and internal linings that keep her hair from growing and let her breathe particulates and eat foods which she'd normally be lethally allergic to. When humanity comes back to pick her up, the first contact is with a suited man who thinks she's one of the Tendu, and she plays along for a bit before saying "I believe the line is 'Dr. Livingston, I presume?'"
A long-running plot point of Animorphs. The Yeerks thought the kids were Andalites.

Live-Action TV

"Tomorrow is Yesterday" from Star Trek: The Original Series.
- Well ... their starship is recognized as a UFO by a fighter pilot, so they pick him up with their transporter (Spock's pointed ears are a shock to him, but he adapts much better than the other guy they pick up later in the episode), then Kirk and Sulu have to go down to an Air Force base, and Kirk gets captured by the military - who don't believe him when he says he's from outer space.
The I Dream of Jeannie episode "U-F-Oh Jeannie", where Tony was mistaken for a Martian by a group of rednecks in the Deep South.
In Kyle XY, Josh Trager claims, half-jokingly, that Kyle is an alien. (In fact he's an experimental clone with psychic powers.) Two years later, when Kyle finally reveals his history to the Tragers, he comments that Josh's guess may have been the closest to the truth.
In the Lost in Space episode "Visit to a Hostile Planet", the Robinsons go back through time to 1947 and are mistaken for aliens when they land on Earth.
In The Addams Family, the Addams are mistaken for aliens by the military, who approach them claiming to wish peace and asking them lots of questions. As a consequence, The Addams believe the army men are aliens as well (because of their green wardrobe).
Stargate SG-1: SG-1 deliberately invokes this when they're stranded in 1969, presumably figuring that it's a quicker explanation than the actual one.
- Quicker, maybe, but the main reason was to avoid paradox. (Although that didn't stop Jack from going by the names of fictional characters, some of whom already existed and others didn't, but who cares? They didn't want to endanger the Stargate program by accident.
Averted in Community. Abed plans to 'mess with' Troy by using the classic sitcom set up for this, except that he didn't fool Troy for a second.
Done in the Torchwood episode "Countrycide", where the team thinks that some aliens are responsible for disappearances and attacks. Turns out, it's a bunch of humanitarians.

Web Comics

The Inexplicable Adventures of Bob played straight and then subverted it, in this strip .
Dangerously Chloe got the male lead replaced with a shapeshifting Succubus when he caught some fever and had to miss the school on a test day. The ensuing weirdness was noticed by a curious student who then tried to date Teddy to find out what's going on. Then she overheard Teddy's "cousin" saying "a normal human date", got it understandably wrong and glimpsed another succubus - in the natural form, with horns and tail. From that moment on, Naomi was inclined to see any weird (and some not weird) stuff that tend to happen around Teddy as more proof that he is a shapeshifting alien. Then she overheard him saying "I'm just not used to being around human girls" in an aside conversation with a succubus. Then an angel Prudence drops in (literally), and since wings and halo are Invisible to Normals, Naomi mistakes her for an abductee - talking about it in euphemisms ("from up there?") doesn't help to clear the situation. And since Prudy is excitably ditzy and forbidden from revealing herself to humans in the first place (besides, the last time it happened, it ended in a lot of headache for her), she does not take steps to disabuse her friend of this notion.
- This gradually moves toward Flat Earth Atheist level, as Naomi persists in this heresy even after visiting Fire and Brimstone Hell.
The Unspeakable Vault of Doom had an investigator of "Alien Abductions" who learned what happened faster than he expected, but still too late.

Western Animation

During the episode "Mush-Rumors" of The Adventures of Super Mario Bros 3, a human family ends up driving into the Mushroom Kingdom by accident and are called aliens by one of the Toads, which then gets spread and exaggerated to the point where Bowser thinks they're an alien invasion force in disguise. The fact that they look not-unlike the human Mario and Luigi never comes up.
There's a The Simpsons episode (The X-Files crossover) where Mr Burns is mistaken for an alien from the results of the various dubious medical treatments he undergoes and glowing green in the dark, a side-effect of working at the nuclear power plant.
SpongeBob SquarePants had an episode with them using Sandy's rocket to land "on the moon" (actually they circle around the moon and land back in Bikini Bottom) and go to hunt "moon clone aliens" which look exactly like their friends on earth.
An episode of The Mask animated series featured a government agent and a scientist mistaking The Mask for a hostile alien due to a series of coincidences (not that it's hard to mistake him as such in the first place...)

Agent: Hmm...Subject has green skin. Imagine! Just like in the funny papers!

Inverted and played straight in one episode of Viva Pinata. Fergie Fudgehog is conned onto going onto a defective rocket ship that crashes. When he comes out, his foggy helmet makes his friends look like aliens to him, and it makes him look like an alien to his friends! Needless to say, Hilarity Ensues.
The Hey Arnold!! Halloween episode. Also doubles as a Parody Episode due to all the Orson Welles references.
In The Santa Claus Brothers, one of the elves is mistaken for an alien.
In the South Park episode "Starvin' Marvin in Space", the people of Australia thought Marvin was an alien. To be fair, he did emerge from a spaceship.
An episode of Gargoyles has an actual alien think the title characters are also aliens.
Invader Zim has an unfinished episode where Zim tricks Dib into thinking Poonchy, Drinker of Hate was an Irken Invader. Hilarity Ensues.
A series of unlikely coincidences cause Candace to beleive that Ferb is an alien. She's obviously wrong, but Phineas and Ferb are helping an alien rebuild his spaceship.
Rocko's Modern Life where he and Heffer think Filburt is an alien after reading his diary. It was All Just a Dream but they were still freaked out
Rugrats did this several times.

Real Life

After Yuri Gagarin became the first human to enter space and return successfully, a woman who saw his capsule land asked him "Can it be that you have come from outer space?" He replied "As a matter of fact, I have!"
- Most likely apocryphal, since it's now known that he actually bailed out of his capsule, and wouldn't have landed near it.
Similarly, when John Glenn was orbiting in the Friendship 7 in 1962, the mission planners weren't exactly sure where the capsule would land - somewhere near Australia, as in any part of Australia or the surrounding oceans or islands for a pretty far distance. Glenn was worried what the aboriginal Australians might think when seeing a man in silver emerge from something that fell from the sky so he took a short speech with him rendered phonetically: "I am a stranger. I come in peace. Take me to your leader, and there will be a massive reward for you in eternity."