Not Quite Back to Normal

A character is unshackled from a Baleful Polymorph—changed back from a frog, cured of their lycanthropy, or just had a Gender Bender undone—but after sighing with relief, they slowly realize that they aren't 100% the same as they used to be. And it's not just because they've walked in another creature's shoes and improved as a person.

Maybe their tongue is a bit longer than they remember, and they have this inexplicable hunger for flies. Or they've still got a wolf tail (and all their friends burst into laughter whenever they turn around.) Or, psychologically, they've retained an uncontrollable fear of cats. At any rate, they've got leftovers.

Usually played for laughs (and often an Ending Trope) but it may be a plot point in a greater arc. Brainwash Residue has considerable overlap.

As an Ending Trope, Spoilers ahead may be unmarked. Beware.

Examples of Not Quite Back to Normal include:

Comic Books

In ClanDestine, Walter's powers involve Hulking Out into a large blue form. When he changes back, sometimes a few body parts remain blue and over sized for awhile.

Film

At the end of Wolf, it is implied that Michelle Pfeiffer's character is infected with Lycanthropy.
Monsters vs. Aliens: A temporary case is seen where Susan is drained of Quantonium and shrunk down to a normal sized White-Haired Pretty Girl. No worries, she fixed it (the size, not the hair color).
In Shrek the Third, Puss and Donkey got their minds switched accidentally. At the end, Merlin switched them back... except for their tails.
In Honey, I Shrunk the Kids, Wayne tests the shrink ray on his neighbor Russell. After being brought back to normal, Russell finds that his baseball cap is a little big for him.
The ending of Young Frankenstein—after the procedure that stabilizes the "monster," the creature has inherited the mild manners of his creator. Frankenstein himself has inherited some...interesting side effects if his assistant's reaction is any indication.
James and the Giant Peach: At the end, even though James Henry Trotter was changed back to a live action boy after remaining stop-motion throughout a majority of the film, the insects that live inside the eponymous giant peach, however, actually stay huge and stop-motion animated.
- Justified: James was transformed when he accidentally swallowed one of the magical "crocodile tongues" that had similarly transformed the bugs (and caused the peach to grow). He reverts to live-action when he coughs up the tongue.
Sinbad and the Eye of the Tiger: The evil sorceress Zenobia doesn't have enough shapechanging potion to turn completely from seagull to human, so spends the rest of the film with one giant webbed bird's foot.

Literature

In the Discworld book Sourcery, Lord Vetinari is changed into a lizard for much of the novel. When he gets changed back, he notices a new habit of sticking out his tongue. This can be a side effect of "Borrowing" (inhabiting the mind of another creature). When Granny Weatherwax does it, she tend to return to her body with some animalistic behaviors and urges. Fortunately, she is iron-willed enough to shrug them off after a while.
- It's shown that the animal habits eventually disappear on their own, as when Esk Borrowed the mind of an eagle and later returned to normal.
In John Morressy's Kedrigern book, A Voice For Princess, although Kedrigern restores Princess to her former self from frog shape, the spell which made her a frog was more complicated than he realized. She becomes a beautiful princess who croaks like a frog.
In The Witcher, princess Adda has spent her entire youth turned into a monster. She looks perfectly normal but still likes raw meat.
In Jules Verne's fantasy novel, Adventures of the Rat Family, the family undergoes multiple transformations, and the comic-relief character always ends up with the tail of whatever the last thing was (for example: they get transformed from rats into fish, he's a fish with a rat's tail). At the end, when they're all human, he's still got an animal tail, and is apparently stuck with it for life.
In Animorphs, Tobias gets Shapeshifter Mode Locked as a hawk in the first book, and gradually his body's predatory instincts begin to affect his personality. Much later, he gains the ability to temporarily turn into his former human form - but he still has the tendency to stare intensely at people like a hawk.

Live-Action TV

An episode of Red Dwarf had Rimmer make his holographic body look like Christine Kochanski in an attempt to manipulate Lister. He still had a boob after he changes back, but was in no rush to get rid of it.
Sanctuary: Tesla is deeply depressed upon being devamped and complains that he's "ordinary." He then realizes he has magnetic powers.
Doctor Who/Torchwood: in The Parting of the Ways, Jack Harkness is killed by the Daleks and then brought back to life by Rose Tyler in her "Bad Wolf" form. We later find out in Torchwood that Jack can no longer permanently die, which seems great, though the Doctor views him as "wrong". It's hinted in Last of the Time Lords that Jack's unnaturally prolonged life will eventually see him mutate into the Face of Boe.

Theatre

John Adams's opera A Flowering Tree is based on south Indian folklore. A girl (named Kumudha in the opera) has the power to transform herself into a flowering tree. She arouses the jealousy of the prince's spiteful sister, who tricks her into transformation and then ravages her, picking all the flowers and breaking the branches. Kumudha is unable to resume human form, and she crawls about the land as a misshapen half-human, half-tree thing.

Video Games

In Monster Girl Quest, "Witch Hunt" sidequest involves a witch turning human girls into tentacled monsters. After the witch is defeated, Luka apparently "seals" the girls' transformations... except not really, and they still can sprout tentacles at will.
The story mode of Soul Calibur V has a serious variant at the end with Pyrrha Alexandra breaking free of Soul Edge's influence. Eyes normal? Check. Voice normal? Check. No longer obsessed with gathering souls for the evil sword? Check. Monsterous Right Arm reverted to something presentable in polite company? Sorry, you are out of luck there.

Web Comics

In Narbonic, Dave manages to get his (and Helen's) Gender Bender transformation cured, but still finds himself attracted to Mick Foley.
Be glad you can't see Torg's "aftereffects" in this Sluggy Freelance strip.
El Goonish Shive had a joke along these lines at the end of the second April Fool's Week storyline. And then again in a side comic storyline.
Eerie Cuties with Ace's misadventures after he wandered out of range before the bimbo curse was removed, and it stuck around. When it got transferred, he looked more manly than he used to. Unfortunately for him, the after-effect later was removed, and his girlfriend got disappointed. Then in a side story it turned out that there's another — he began shapeshifting into a girl, with Jekyll and Hyde style personality split.
Sanity Circus shapeshifters choose one animal as the target shape and spam the spell until success. After a while they can shift without a spell, but there are visible traces in the human form. Eventually a shifter is stuck somewhere between the two, thus becoming an ex-shifter — like Donovan Sparc or Abbie (that crocodile councilwoman). It's common enough that In-Universe nobody asks how this happened or comments on such an appearance (Nimbus did once, when he was nervous, but it was regarded as childish by everyone including himself). Fletch did elicit a comment behind his back once, to the effect that he must have shifted far too much to have feathers for hair at his age — and a joke from his archer friend, which is how he got this nickname.

Western Animation

An episode of Futurama gave Bender a sex change. When Farnsworth turned him back to normal, he found that he had become more in touch with his "feminine" side (but denies it).
The Powerpuff Girls: The Freaky Friday Flip episode has many different body swaps going on, but eventually everyone seems to be back to normal- except that at the end it turns out Bubbles' body was still swapped with the Narrator.
In an episode of The Legend of Zelda animated series, Link is transformed into a frog. At the end of the episode, after he is cured, he still reflexively grabs and eats a fly.
In Duck Amuck Daffy ends up completely erased by the sadistic animator and testily asks to be redrawn. He gets his wish in the worst way possible, but it's not until the animator draws a mirror in front of him that he notices (including the fact that he's inexplicably gone quadruped!).
In Grim And Evil episode 5 during the Evil Con Carne segments Devolver, Part 1 and Devolver, Part 2, General Skarr keeps devolving into different species due to accidentally being exposed to Major Dr. Ghastly's devolving ray. In the end, Ghastly and Hector manage to expose Skarr (who has become an amoeba by that time) to a re-evolution ray, turning him back to his normal self... except he still has a monkey tail (though only Hector and Ghastly seem to notice it).
In The Emperors New Groove the villain, Yzma, is transformed into a kitten in the end. By the time of the sequel, she is human again, but still possesses a tail and some catlike behavior (which is an Actor Allusion; Eartha Kitt is best remembered for playing Catwoman)
In one episode of The Life and Times of Juniper Lee, Juniper is turned into a lemur, but when she is changed back at the end of the episode, she still has a tail. Psych, no it was just Ray-Ray telling her she still had a tail.
One Treehouse of Horror episode had Homer Simpson get turned into a bizarre chimera with a chicken's body. When homer turns back to normal at the end of the episode, it turns out that he still has the body of a chicken... and lays an egg.
American Dragon: Jake Long: In one episode, a soul-sucking nix sucked the souls of several students during a school dance. In the end, everything went back to normal. Except that Trixie and Spud were now in each other's bodies. They were back to normal in the next episode but it's never revealed how they did it and it was never been brought up again. (note: It happened before they learned about Jake being a dragon)