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Iron Man used to be known for body guarding Tony Stark. On an occasion where he couldn't take off the suit, Stark's disappearance made people suspect Iron Man.
In "The Monster From Krypton", red Kryptonite transforms Superman into a dragon-like creature called a drang. When he holds his cape to communicate the change, Jimmy Olsen thinks the monster killed him and alerts Supergirl and the army.
In Swamp Thing, government agent Matthew Cable, encountering the title character for the first time, believes that he's Alec Holland's murderer. Eventually the Swamp Thing manages to convince him that he is Holland or so he and everyone assumes prior to the Alan Moore retcon.
Princeless: Princess Adrienne's Dad thinks she was killed by the mysterious knight who destroyed her tower. The knight is Princess Adrienne.
Film - Animated
In Brave, Fergus stumbles on Elinor's torn dress and then on her bear-self attacking Merida. He nearly kills her before he discovers who she is.
In Brother Bear, Kenai and his brother Denahi are tracking down the bear who killed their oldest brother Sitka. Kenai corners the bear and kills it, but the spirits turn him into a bear directly afterwards. When Denahi arrives on the scene, he sees Bear!Kenai and thinks it is the bear that killed Sitka, surmising that it killed Kenai too. He spends the rest of the movie tracking down Kenai to kill him for...killing Kenai.
Invoked by Yzma in The Emperors New Groove. She tells the guards that Pacha and Kuzco (who has been turned into a llama) murdered the emperor (Kuzco).
Kuzco: No, wait I'm the emperor! It's me Kuzco!... They're not listening!
In Shrek, Donkey thinks an ogre ate Fiona after he finds one in her room. She calms him down enough to tell him that it's her curse.
In the Sherlock Holmes story "The Man With The Twisted Lip", the titular man is actually the gentleman he was accused of murdering in disguise. A rare example where he was not trying to prove his identity. He didn't want to shame his family with the revelation that he'd been begging as an occupation.
When Eustace from Voyage of the Dawn Treader wanders away and is involuntarily transformed into a dragon, his companions frantically search the island for the missing boy. On first sighting Eustace as a dragon, they initially assume he's the monster that ate Eustace, although he's able to prove his identity with body language.
Buffy the Vampire Slayer: In "A New Man" Giles has been transformed into a Fyarl demon which is thought by the gang to have killed Giles.
Buffy: (stabbing Demon!Giles) This is for Giles!
Giles: (in demon language, which only Spike understands) For me?
The Incredible Hulk is suspected in the death of David Banner, because no one knows Banner's secret.
In the Are You Afraid of the Dark? episode "The Tale of the Hunted", while on a hunting trip, Diana gets turned into a wolf. Her father sees her wolf self in her cabin and assumes she killed her. Diana evades the hunting posse until the transformation wears off.
A non-murderous variant occurs in Dario Fo's play Trumpets and Raspberries, in which an industry mogul is under arrest for his own kidnap after a case of Mistaken Identity followed by restorative Magic Plastic Surgery.
Exploited by the head of the monsters in one area of Dragon Quest VII. It strikes a deal with the local priest, claiming that as long as the priest lives in a cursed, monstrous form, it will leave his hometown and everyone living there alone. However, the transformed man is forced to return home and try to live among the residents, who naturally tend to assume that he killed the real priest and is mocking them. In other words, the monster expects them to invalidate the deal by killing the transformed priest themselves, at which point it can swoop in and finish them off...
On Buzz Lightyear of Star Command, Buzz and Mira are exposed to Zurg's latest evil concoction that transforms and fuses them into a single amorphous blob creature unable to talk. When Booster and XR find the blob next to Buzz and Mira's empty uniforms they assume it ate them.
In the Futurama episode "Leela's Homeworld", Leela thinks the mutants who spied on her killed her parents, when in fact they were her parents.
On Sponge Bob Square Pants, SpongeBob and Patrick fall in love with one of Sandy's pets, a caterpillar named Wormy. When Wormy transforms into a butterfly overnight, they, having never seen such a thing, assume it's a monster that ate Wormy... and they were next!