Mistaken for Masturbating

According to popular belief, some groups of people - teenagers, loners, men of all kinds - masturbate a great deal. A character who locks himself in the bathroom or in his bedroom therefore raises the suspicion that he's masturbating, even when he's doing nothing of the kind. The character may well be hiding something else so carefully that he can't or won't clear up the mis-assumption. Hilarity ensues.

Anime & Manga

 * Bleach: Ichigo's father jokingly considers this when his son is talking to ghosts in his room.
 * Death Note: Light deliberately invokes this trope to conceal the fact he's killing people with a magical notebook.

Comics

 * Inverted in The Adventures of Barry Ween by Judd Winick. When asked by his parents why he's been in the bathroom so long, he shouts back "Go away, I'm masturbating!"; while trying to dispose of the results of his latest failed experiment (which stubbornly keeps trying to climb back out of the toilet).
 * Again inverted: in the Gen 13 reboot by Gail Simone Grunge has been shown as being a geekish, mommy-boy kid. Wanting to "reinvent himself", he cleverly and systematically rebels against it, for example disposing of all his anti-asthma medications, vitamins and dietary supplements in the toilet while faking a double-entendre laced Immodest Orgasm just to mess with his family.

Film

 * The scene from Transformers where Sam Witwicky's parents notice that he's hiding something from them in his bedroom. Sam can't tell them that his 30-foot-high transforming robot buddies are right outside the window, of course, and so hurriedly tries to get them to leave the room. Sam's mother outright asks if he's masturbating. When the outrageously hot Mikaela pops out from his closet, they quickly end their suspicions and congratulate him. In the Riff Trax commentary, Bill Corbett's suggestion definitely outdoes Mrs. Witwicky's "Sam's Happy Time" euphemism: he casts his ballot for "LaBeouf Strokinoff."
 * There's Something About Mary: Ted Stroehmann is daydreaming in the bathroom but is accused of masturbating to Mary, who is changing clothes in a room in view. Hilarity Ensues.
 * In Mercury Man, Chan, in testing how his body becomes fiery hot whenever his heart beats fast, looks through a girlie mag and his clothes burn off — just as his mom walks in the room.

Literature

 * In Theodore Sturgeon's post-apocalyptic story Thunder and Roses, the marine narrator thinks the creaking cot behind him is because his bunkmate is enjoying the singing star's broadcast immensely. The bunkmate is actually committing suicide.
 * In a variant, in The Throne Of Bones (no, not that kind), an in-universe author of horror stories complains that ignorant people sometimes assume his stories are for real. Among these is a tale in which he's harassed by a deformed monstrosity that arose from the semen he'd deposited while masturbating.

Live-Action TV

 * In one episode of Skins, Anwar's mother knocks on his bedroom door, asking "Anwar? Are you masturbating?" (He isn't.)
 * An episode of Modern Family had a couple debating whether to confront their son about his mysterious, private activity in his room. It turns out that he's... hanging upside-down to try to grow taller. The father scoffs at how much the son paid for the growth device - "He could have bought a 2-year subscription to Playboy with this!"

Video Games

 * One of the video recordings in Persona 3 shows Fuuka using a stomach slimmer that goes into overdrive, tickling her uncontrollably. At that moment Mitsuru knocks on Fuuka's door to hear her panting and hurriedly shout "I'm coming!", complete with humming sound in the background...

Web Original

 * Ghost will sometimes assume a caller is "playin' with their peter-popper" if they do not respond when brought on

Western Animation
"Krusty: Close the door!"
 * In Family Guy Chris was once really just using the bathroom, but his Holier Than Thou grandfather assumed he was masturbating and railed against its sinfulness, scaring poor Chris away from what he was really doing for the rest of the episode. "God's watching me do Number Two? Aw man, I'm a sinner and God's a pervert!"
 * In a pre-cancellation episode, after Chris is caught peeping in the girls' locker room, Peter approaches Chris' room, and there's a rapid knocking sound, which turns out to be Chris, playing with a ball-and-paddle. Peter gives Chris his porn collection, then leaves, and the sound continues, then Peter realizes he's holding the paddle.
 * In The Simpsons episode "Like Father Like Clown", it is implied that Krusty's father thinks he is masturbating in the bathroom, it turns out he was doing a comedy routine with a spray bottle.

"Dr. Venture: (knocking on bathroom door) Dean, what the hell are you doing in there? I need to take a shower!
 * In the King of the Hill episode "The Son Also Roses" Hank is suspicious as to why Bobby is spending so much time in his bedroom closet, it is implied that he thinks he is doing this, he is actually growing roses and he's hiding it because he didn't want Hank to find out.
 * In another "Hank's Dirty Laundry" someone has been renting porn using Hank's name and getting fined for not returning one of the videos, the actual culprit we later find out is actually, at one point the culprit sends him some video tapes to provide clues that he did not rent them Hank locks himself in the bedroom to watch them Peggy walks in on him thinking he was masturbating and runs out, he was actually fiddling with a pencil while taking notes on the videos.
 * In The Venture Bros, Dean practises kissing kissing on his hand while imagining it's Triana, which leads to a misunderstanding with his father:

Dean: I'm practicing being a boyfriend, pop.

Dr. Venture: (recoiling) Nevermind, Dean."