Mistaken for Spies

The characters arrive in the Adventure Town, just as soon as something nasty happens.

Odds are, they will end up getting accused of doing it and/or being enemy agents and temporarily incarcerated for it.

More common in the Cold War era, or in shows that travel back to that time.

Examples of Mistaken for Spies include:

Anime and Manga

Soukou no Strain with some rather justified suspicion being thrown at Sara after her identity is revealed. The big bad is her brother, after all.
The anime version of Sailor Moon has Ami Mizuno first being mistaken as an agent of Queen Beryl's before she is revealed to be Sailor Mercury.
Happened to Tsukune in Rosario + Vampire when the school thinks he is a spy for humans attempting to destroy the Monster World.

Comic Books

In one of the time-travelling strips from Archie Comics, Jughead ended up in the middle of the Civil War and was immediately accused of being a spy for the South until Lincoln himself pardoned him.
In The Warlord, this happens to Mariah when she is accidentally stranded back in the USSR after spending years in the Lost World of Skartaris.

Film

North by Northwest.
The Tall Blond Man with One Black Shoe, a French comedy where the title character, an innocuous concert violinist, is marked as a spy by infighting government high-ups - he's blithely unaware of being a pawn in their scheming through the film. Played pretty straight-faced; the American remake, The Man With One Red Shoe, was considerably broader.
Wallace Ritchie from The Man Who Knew Too Little is mistaken for a secret agent by just about everyone. He doesn't mind, because he thinks it's all a play, with him cast in the role of a secret agent.
François in the Timeline movie.
- While this is the reason given for killing him, this troper got the inpression this was just an excuse, given that the English Lord who has him killed is an evil Jerkass.
Plot of the otherwise forgettable If Looks Could Kill.
Subverted in the James Garner film The Pink Jungle. He goes through the whole film insisting that he's not a spy, just a fashion photographer. At the end everyone is finally convinced he's just a photographer, and then in the final scene, it's revealed he's really a spy.
Played straight in another James Garner film A Man Could Get Killed.
Tom Hanks in The Man with One Red Shoe.
The protagonists of Hot Tub Time Machine after their twenty-first century technology is stolen.
Dumb and Dumber.
Minor variant in Moscow on the Hudson. Robin Williams' character, a Soviet defector, is being followed by a man in an overcoat down a street. Robin Williams confronts him and demands to know why he's being followed and if he's from the FBI, CIA, or KGB. The man calmly replies he's G-A-Y to which Williams' realizes what he means and laughs.
The plot of Cars 2 involves British intelligence agents mistaking Mater for an American ally.
Jackie Chan's role in The Tuxedo.
In The Big Lebowski, The Dude is mistaken for a private detective by Delfino, another private detective who is searching for Bunny Lebowski.

Literature

In Brave Story, Wataru reaches the first Adventure Town just in time to be framed and imprisoned for a murder/theft. Fortunately(?), another attack that appears to be perpetrated by the same individual(s) happens while he's in jail, so the local law enforcement realizes he can't be the culprit and lets him go.
Happens to Barney in The Dark Is Rising, where he has the misfortune of being caught in Owain Glyndwr's camp while being English. Luckily for him, Merriman is on hand for a rescue.
Evan Tanner in Lawrence Block's The Thief Who Couldn't Sleep was just trying to steal some gold when an agent (killed shortly afterward) apparently mistook him for a contact and handed over some vital documents. Hilarity ensued, leaving Tanner with a reputation as a resourceful and dedicated agent for a very ~~disorganized~~ free-wheeling U.S. intelligence agency (even the agency's boss thought so). As Tanner put it in one of the later books, when the CIA took custody of him, he kept telling them he worked for somebody else who'd eventually come to bail him out—but he was more surprised than the CIA was when the somebody else did come.

Live-Action TV

Chuck does this quite a bit. Morgan, Captain Awesome...
Doctor Who had this happen so often, some of the audio dramas started doing a Lampshade Hanging on it.
Stargate SG-1: In the episode "1969", a freak Stargate accident sent SG-1 to a missile silo in the titular year. Naturally, strangers materializing in a high-security area would likely be Mistaken for Spies; Daniel's responding in Russian to a question asking (in Russian) whether they were Russian spies didn't help matters much.
- The same thing happens at least twice more in later seasons on alien planets. Again, it's a case of strangers materializing in a high-security area, although the circumstances are a bit different. In "1969", a freak accident sent them to a missile silo in the past: the location of the stargate in the present day, but it wasn't there yet. In similar episodes later, they traveled to worlds where the Stargate had been found and was recognized as being important, but the locals hadn't figured out how to use it yet. Sometimes, some locals believe the team's story of being aliens who came through the religious artifact or museum piece or whatever they think the Stargate is, but other times, the locals jump to the conclusion that the team is attempting to steal or deface the Stargate or spy on something else of value in the same facility.
Star Trek: In original series episodes "Tomorrow is Yesterday" and "Assignment: Earth". Also in the movie Star Trek IV: The Voyage Home, where the Russian Chekov is captured on the aircraft carrier Enterprise.
- Of course, in Star Trek IV, Chekov and Uhura did just beam in to the reactor room of an aircraft carrier to steal some of its energy.
- It was a good ten years before this troper knew enough about the world to realize just how mistaken a decision sending Chekov to scope out "nuclear wessels" was.
In Goodnight Sweetheart, Gary is pretending to be a British spy. In one episode, however, the fact British Intelligence don't have him on file leads them to briefly suspect he's a German spy.
Happens several times to the heroes of The Time Tunnel.

Theatre

Pretty much the plot of the WWII musical Kilroy Was Here.
Also the entire plot of Woody Allen's play Don't Drink The Water.

Video Games

Can happen to anyone in Team Fortress 2, especially if you're among Pyros, who are tinfoil-hat wearing insane with paranoia. At least in Team Fortress 2, you can't hurt your own allies, so it's prudent to attack everyone in sight with your weapon of choice.
- The "Meet the Spy" video features this trope with the BLU Spy being mistaken for the RED Spy. In this case, however, the characters can hurt their allies...

BLU Spy: He could be you! He could be me! He could even be—(head explodes)
BLU Soldier: (having just fired his shotgun) What? It was obvious! He's the RED Spy! Watch, he'll turn red any second now. (beat) Aaaaaany second now...

Done to Tear and Luke in Tales of the Abyss.
This happens to your party in Final Fantasy V in Karnak. When you visit any of the shops, you find the prices for the equipment are unusually low. However, as soon as you try to purchase anything, your entire party is taken and thrown in jail in a cell next to one containing Cid, the inventor of the crystal amplifier. It turns out that one of the guards saw your party emerge from the meteor and thought them to be in league with the monsters.

Web Comics

In Order of Tales, Koark goes to Tenshells to visit Extranji, and finds the man mortally wounded. Upon leaving the house, Koark is accused of killing him and arrested.

Western Animation

The Hunchback of Notre Dame: Happens to Phoebus and Quasimodo when they try to sneak into the Court of Miracles to warn the Parisian Gypsy community of Frollo's imminent attack. Considering that both men were very heavily associated with Frollo, it's no wonder they were accused of espionage. Oh, and the entire accusation is a musical number.
In the very first episode of Avatar: The Last Airbender Sokka accuses Aang of being a Fire Nation spy. And in the fourth ep. The Warriors of Kyoshi Aang,Katara and Sokka are accused of being this.
In part 2 of the series premiere of My Little Pony Friendship Is Magic after Nightmare Moon took over, Twilight Sparkle was the only one who actually knew who Nightmare Moon was, thanks to her reading a book of Equestrian legends that pretty much told how Nightmare Moon would escape and when. After Twilight runs back to the library that was her house to look up more information, a suspicious Rainbow Dash briefly accuses her of being a spy.

Real Life

Happened to a delegation sent to a Muslim town by Genghis Khan. They were promptly massacred and their goods stolen, Khan wasn't amused, and the slaughter of cities ensued.
- How is that hilarious? Was it all done to the Benny Hill theme?
  - Yes.
A trio of American hikers that have been detained in Iran because the government thinks that they were spies. The penalty for spying is death and the one woman that they've released will be trialed in absentee if she doesn't return, and naturally Iran is under a lot of international pressure to not do anything stupid (like killing three more than likely innocent people because of mindless paranoia).
- Turns out that they were sentenced to something like three years in prison. Not enough to provoke the US into invading, but enough to seriously piss people off.