In All Fall Down, the shape-shifter Phylum, while entertaining children in hospital, is permanently trapped in the form of a chimpanzee.
Walter Langowski/Sasquatch from Alpha Flight is a gamma mutate with the power to transform at will into, well, a Sasquatch. Over the years, however, he's spent more and more time as Sasquatch, hardly ever reverting to human form. By the time of Immortal Hulk, its started to become actively painful and difficult for him to turn back into a human again, prompting him to seek out Bruce Banner (who has experience with this trope) for help, fearing that soon he won't be able to transform at all. His fears are proven horribly true when it's revealed that his difficulty shapeshifting is the result of Brian Banner gradually influencing and possessing him from beyond. He is only restored back to humanity when Hulk manages to drain his gamma radiation and Brian with it.
Big Bang Comics: The Hummingbird, who was shrunk by an alien ray that was destroyed before he could be re-enlarged. As such, he's stuck permanently at a maximum height of six inches, though among his powers is the ability to temporarily shrink even smaller.
In Billy Batson and the Magic of Shazam, Tawky Tawny is reimagined as a spirit who can shift between a human and various animal forms, usually a tiger. When fighting Niatpac Levram (aka Mr. Mind), he tries to transform but gets hit, which, due to the instability of magic at the Rock of Eternity, traps him halfway between human and tiger shape, making him an anthropomorphic animal like his counterpart in most other Shazam! books.
Black Hammer: The superheroine Golden Gail used to be able to change from a grown woman to a superpowered child and back again by saying the magic word "Zafram". Then she and the other heroes wound up trapped on a mysterious farm after defeating the Anti-God, where she discovered that the word had stopped working. She's been stuck in the form of an unaging nine-year-old for the last ten years, hating every second of it.
Doctor Strange foe Dormammu's sister Umar used to be the Stronger Sibling. Then Umar gave birth to her daughter Clea while transformed as a human. To Umar's chagrin, this locked her into human form forever, which made her weaker than her brother.
ElfQuest. The female High One named Timmain regularly changed into the form of a wolf to hunt. She eventually forgot her true identity and came to think of herself as a wolf.
Happens to the Hulk on occasion. Whether this is good or bad depends on the form he's stuck as. Hulk would love to be mode-locked and never turn into Banner again. Banner would love to be free of the Hulk, but at this point knows better. Both absolutely hate the idea of being mode-locked as the other.
The Abomination is completely incapable of returning to his original human form, and he's none too happy about that.
In Justice League: Generation Lost, it is revealed that Captain Atom had lost the ability to change back and forth between being Captain Atom and Nathaniel Adam/Cameron Scott. It was introduced out of the blue, as no previous appearance had even suggested that he was losing the ability to transform effortlessly, so it did not have much dramatic impact.
The Big Bad sent a shapeshifting demon to kill Elaine. The demon in question killed her father and took his form to get close to her. After Elaine escaped, the Big Bad decided to stop said demon from interfering by trapping it in that form permanently. It literally begged for death at the end, as the man's memories started to overwhelm it.
Jill Presto doesn't know that Mazikeen's half-rotted face isn't an injury but a deliberate shape-shifting choice, and tries to "heal" it with the power of the Basanos. This trope is the result. Mazikeen is not pleased.
Other instances include Manhunter being reduced to amorphous goo by a neurotoxin, being trapped in Aquaman's body and freaking out, and an Elseworlds story where all the heroes lost their powers, leaving him in his natural Martian form with all of the suck and none of the blessing.
The evil White Martians are initially dealt with this way by the JLA. They are given human form and have their memories removed, effectively trapping them as humans. Needless to say, problems occur when a few of them get their minds back and remember how to shapeshift.
Parodied by the She-Hulk graphic novel. Jennifer is told by Reed Richards that he has bad news: She's stuck as She-Hulk forever and can never change back into regular human Jennifer. After a Beat Panel, She-Hulk inquired "So what's this bad news"?
A Skrull named Khn'nr was to be used in the infiltration of Earth in Marvel'sSecret Invasion event. He was mode locked into the form of Captain Marvel, a long dead hero, and brainwashed into thinking he was him from the past. When he found out, he rejected his part in the invasion, and now is trying to work against it.
Quite a few Skrulls who took the form of Dr. Hank Pym wound up losing themselves in the role/being overwhelmed by the personality of the original, and had to be put down.
During the period when the entire Skrull race lost their powers, they were stuck in whatever form they took at the time. Those whose jobs involved snaking through drainpipes, for example, had to be cut out. The villain who actually initiated the change was in a suit that he thought would protect him from the effect. It did not, leaving him permanently trapped inside, in agony because the "suit" was not hollow, but loaded with internal machinery that he had oozed around and between.
Some Skrulls who invaded Earth were brainwashed into becoming cows, rendering them harmless. Unfortunately, the cows were then slaughtered, and those who ate the meat either died or gained powers along with a virus. That's the origin of the Skrull Kill Krew. Team member Riot was stuck in a monstrous bug form for an extended period of time.
In Who Took the Super out of Superman?, alien villain Xviar takes on human form in order to mingle with Earth people, but due to a flaw in the process he's unable to change back to his original form. His body can't age either, so Xviar is forced to move and change jobs constantly so nobody wonders why he doesn't get older.
"The Unknown Legionnaire": Brainiac 5 accidentally sprays Chameleon Boy and his pet Proty with Cancelite (a chemical invented by Supergirl which prevents Durlans like Chameleon Boy from shape-shifting), making them unable to change shape during their current mission.
"Those Emerald Eyes Are Shining" involved Durlan shapeshifter Chameleon Boy getting stuck in his usual form and undertaking a dangerous journey on Durla to a place that would restore his shapechanging abilities. His father, who had long ago been locked into human form by a disease, came with him, but only to provide support; he had adjusted to having a permanent form and didn't want his abilities back.
The Legion of Super-Heroes' clubhouse itself was originally an alien called Fortress Lad who had the ability to turn into a fortress. Fortress Lad was rejected by the Legion, who were then attacked by Mnemonic Kid, who had the power to erase memories. She blanked the memory of the Legionnaires but Fortress Lad stepped in before she could do further harm, transforming into a building to protect them. In retaliation, she proceeded to attack him, entirely erasing his memory of being a living being, only one thought in his mind ("Never give up") leaving him locked in building mode forever. When the Legionnaires regained their senses and defeated Mnemonic Kid they simply believed the building already was their clubhouse, since they had a feeling of fondness for it.
In a Spotlight issue, Soundwave gets locked by the Decepticon Pretenders when he tries to stop them after learning the full extent of their plans.
The Dinobots, who took their alt-modes to avoid succumbing to energon-poisoning. However, due to circumstances, they become unable to ditch these afterwards. Grimlock tries, and the most he can do is make a few cosmetic changes. By the time they get a chance to change them, they've all decided they like turning into dinosaurs.
There's a device that locks a Transformer in one mode. It's used on Blaster for defying Grimlock. It's more than an inconvenience for Blaster (or Soundwave, for that matter) because of their alternate modes: not-terribly-mobile radios. It later gets used to mode-lock the Combaticon Blast-Off in his space shuttle mode in order to take a bunch of human kids for an orbital joyride.
Toward the end of the Marvel run, Grimlock searches for a legendary energy source, Nucleon, to revive several fallen Autobots for the upcoming battle with Unicron. After the battle, he froze up, his body reforming into a new Action Master form - one which couldn't transform (see the Toys entry below for more). Other Autobots weren't immediately affected; in the IDW follow-up series Regeneration One, we learn that some of the revived Autobots had unpredictable, dangerous side-effects, and Grimlock set out on a quest to find a cure, which set the second story arc in motion.
The series introduced the Militant Monoform Movement, a radical group that believed that alternate modes were a form of literal social engineering and should be outlawed. The group's main method of enforcing this seemed to be removing transformation cogs, sometimes not willingly.
Tarn, the leader of the Decepticon Justice Division, is so addicted to transformation that he burned out his T-Cog, requiring a replacement to be transplanted to allow him to retain the ability. In fact, he required many transplants because of how quickly he kept burning the replacements out, and teamed up with the corrupt Autobot medic Pharma, who was a serial killer that sold Tarn the T-Cogs from his victims.
In a Flash Forward issue looking at Ironhide in a peaceful future he mentions that he is likely unable to assume his vehicle form anymore as a result of his advanced age.
Transformers (2019): When Leviathan falls into a sudden fissure in her vehicle mode, she insists to the group that shows up to investigate that she's stuck because she's suffering from mode lock. The truth is that she's just so attached to her vehicle mode that she refuses to assume robot mode until a group of Ascenticons arrive and attack the others.
Wonder WomanVol 5: Circe manages to trap Deimos and Phobos, who often disguise themselves as dogs, in the form of a pair of Doberman Pinschers. They are utterly furious that she would dare, and even more angry that they are now magically trapped as Veronica Cale's obedient pets.
In the Gambit solo series, Courier shapeshifted into a woman to make an appointment with Mr. Sinister, who was posing as an obstetrician. Realizing he was set up, Sinister injected "her" with a destabilizing agent, the only antidote for which was to take away her powers completely. Unfortunately, he didn't realize Courier wasn't originally female...
Courier's not the only X-character to suffer this. Nearly any character with a civilian form and a combat form will find him/herself stuck in powered-up mode. Colossus has been trapped in metal form, Iceman in ice form, Lifeguard in half Shi'ar form, Shadowcat as intangible (not shapeshifter but worth mention), Wolfsbane as at least part wolf, and so on.
