In general, pretty much all mutants* With a handful of exceptions like Kitty Pryde and Quicksilver have the scope of their comic powers massively toned down (more so than even the MCU and DCEU) largely to fit the more grounded tone of the universe. Considering there's multiple characters who have planet or solar-system level powers this can be seen as a pragmatic choice.
Cyclops' abilities are nowhere near his comic book counterpart's. Not only are his leadership capabilities at the barest minimum, but he also seems to lack any form of hand-to-hand combat training. In addition, his optic blasts, unrestrained, are the strength that Comic!Cyke sets as his default. Comic!Cyke's unrestrained optic blast is the X-Men's equivalent of a smart bomb and basically wipes out anything in his field of vision.
In the movies, Wolverine's Healing Factor has been nerfed such that he is no longer immortal. In X2: X-Men United, Wolverine could literally be knocked out by a single shot (albeit one that is well-aimed and has great stopping power) while his comic-counterpart's Healing Factor has always varied Depending on the Writer, that is kinda pushing it... However, the writers apparently realized this, and in the next few films, he's able to survive multiple gunshot wounds and even partial disintegration. It gets even weirder when, in The Wolverine, he survives a nuke in a flashback scene took place beforeX2. Furthermore, Wolverine can be still killed by decapitation as his regenerative ability cannot heal entire body parts.
Jean Grey, whose telekinesis gives her the ability to... levitate a single object at a time... if she tries really hard. Oh, and throw frisbees. Needless, to say, the comics version can do a lot more than that, even without the Phoenix Force. Jean can also only use Cerebro for only a few seconds before passing out, in the comics she easily gets the hang of it and eventually can use it more effectively than Professor X can. The new timeline Jean isn't any better, as in Dark Phoenix as powerful as Jean is she's still pretty much the mutant equivalent to Carrie, compared to the planet-busting Phoenix of the comics who has gone toe to toe with Galactus.
Storm is embarrassingly pathetic compared to her comic counterpart. Hell, she can only utilize the full extent of her Weather Manipulationwhen she's outside unlike the comics where she can shoot lightning from her hands anytime she wants. In the first movie Storm is overpowered and knocked down an elevator shaft by Toad. True she gets a Heroic Second Wind but the fact Toad is able to taunt and intimidate Storm despite her being far more powerful than him is very telling. The sequels don't do Storm any favors either; instead of blowing her foes to kingdom come, she only ever provides cover and support to Wolverine and co. Sometimes she summons a lightning bolt or two but that's it.
A particularly sad example is Rogue in X-Men: The Last Stand. In the comics, she started out as an insecure and depressed girl who didn't have control over her powers but grew into them and become a self-confident badass. The first film had her as the insecure, depressed girl, and the second took steps to develop her power control and confidence... only for a change in directors to completely neuter this storyline in the third movie and make her just as weak as she was in the first film and ending with her removing her powers altogether. Furthermore, in the comics she has super strength and flight which she gained after permanently draining the energy of the superhero Ms. Marvel, while in the movie she lacks these abilities completely. Anna Paquin has said this is one of her biggest regrets with the role, as she really wanted to fly and kick some ass at some point.
Jubilee, as while her “glittery fireworks” powers seem lame in the comics, they are actually “Lumikinetic Explosives” which at full power can can destroy an entire forest and has the potential “detonate matter at a sub-atomic level” like a h-bomb. In the films Jubilee’s power are lame, seen in X-Men: Apocalypse where all she does with her power is short circuit a arcade machine to get some quarters back to Jean. It also doesn’t help that Jubilee was almost entirely Demoted to Extra, only showing off her powers once before in a Deleted Scene in X2: X-Men United where she makes sparks come out of her fingers, which again is a highly underwhelming display of her mutant power.
Magneto in the comics naturally possesses some resistance to telepathy, but X-Men: Days of Future Past shows that he's completely vulnerable to Xavier's power if he doesn't wear the helmet. Moreover, Emma Frost was able to enter his mind and access his traumatic childhood memories, causing him to collapse in extreme pain. His power set is also limited to being able to telekinetically bend and move metal as opposed to using various magnetic abilities (such as his use of force fields).
Speaking of Emma Frost she gets this twice, in X-Men Origins: Wolverine she's just a glorified bullet shield with her diamond powers and in X-Men: First Class her telepathic abilities are much less potent compared to comics (where she's on par with Jean Grey). The aforementioned Magneto defeats her in a diamond form with a bedstead and in Days of Future Past she's unceremoniously killed offscreen.
Keniuchio Harada gets this hard in The Wolverine. In the comics he is the Silver Samurai as well as a mutant who can generate tachyon energy from his body allowing him to cut through almost everything with his katana, he’s matched his Worthy Opponent Logan on numerous occasions. In the film thanks to the Silver Samurai being a Decomposite Character Harada isn’t the samurai with Ichirō Yashida being the real Silver Samurai instead (though his powers are different in that he’s got Powered Armor and not a mutant) whilst Harada is just a human Badass Normal who effortlessly gets his ass kicked by Wolverine multiple times.
Deadpool is regarded as one of Marvel's best comic book anti-heroes because he's a crazy reality alteringAx-Crazy assassin who is nearly unstoppable. In X-Men Origins: Wolverine, he's downgraded to Colonel Stryker's attack dog, without permission to speak or even think for himself, doing whatever his boss says without question. Eventually, he gets his mouth sewn shut and his brain built with cybernetic implants that makes him Stryker's entirely remote-controlled, robotic servant without free will or his own skill whatsoever. Because Stryker is in control over Deadpool, the former causes the latter to lose easily to Wolverine and Sabretooth after they decapitate him. However, his solo film redeems him after the writers realized his wasted potential.
In Deadpool 2, one of the final threats to show up is Juggernaut. Though he's depicted as very powerful, able to smash through obstacles, lift buses and overwhelm Colossus, he's far from invincible and eventually gets knocked out by a Big Damn Heroes moment from NTW and her girlfriend, something his comics version likely wouldn't have even been slowed down by. Admittedly, he gets back up minutes later.
It's fair to note that Cable technically gets this in Deadpool 2 as well, despite Josh Brolin's badass portrayal. In the comics Cable actually has powerful psychic abilities (since he's Jean Grey's clone's son), while movie Cable really only uses guns and his cybernetic arm, instead of any telepathic powers* At one point he does summon his gun to his arms, which may be telekinesis but it could also be magnetism . Cable is also repeatedly matched in combat by Deadpool, even when Wade was wearing a Power Nullifier, while in comics Cable can often demolish Deadpool without any effort.
Barring Domino, who stays as dangerous as ever, and Peter, who just showed up for the ad, the members of X-Force all go through this. In the comics, though they're considered C-list, they're all at least reasonably competent. In the movie, they're depicted as Super Zeroes who end up dying in Bloody Hilarious fashion within less than a minute of their first mission.
Sunspot probably gets hit with the hardest with this out of all the team. In the comics Roberto is easily one of the most strongest mutants period due to being able to convert solar energy into physical strength, letting him lift well over 50 tons (if not more) as well granting him flight, Thermokinesis and Photokinesis. In the film, Sunspot can’t fly, can’t manipulate solar energy and at best lifts a chapel bench in the climax and easily gets pushed into a pool by Dr Reyes with just a broom. His powers appear to be fire based instead of sun based as well, making him a discount Human Torch.
Cannonball spends most of the movie terrified of using his “Thermo-Chemical Energy” powers but even when Sam does use his power, it’s nothing to write home about compared to the comic. In the comics Cannonball is a Flying Brick with his “blast field” being able to act as a force field that can protect himself and trap his enemies, and he’s defeated the likes of Gladiator. In the film we barely see Sam fly and he’s knocked down fairly easily by the Demon Bear in the climax.
Wolfsbane while she lacks flashier powers of the aforementioned boys is still no pushover in the comics. Besides her lycanthropy, Rahne has a variety of powers such as enhanced senses, enhanced vision, a Healing Factor and later gets a secondary mutation that allows her extend her claws like Wolverine and can even split herself into a a pack of five wolves. In the film Rahne just gets hairy and feral, even Dr Reyes can throw her off when Rahne jumps on her back and starts clawing. Worse still she doesn’t help out in the climax beyond carrying an unconscious Dani around and giving her moral support.
Lockheed, in the comics he’s not just the Team Pet and is actually an incredibly powerful little dragon having fought the Brood and survived Secret Wars (1984). In the film, he spends most of the movie as Illyana’s Sock Puppet and then her summoned familiar and displays no real independent intelligence like the comic version.
The most egregious example by far however is the eponymous villain in X-Men: Apocalypse, in the comics En Sabah Nur is right up there with the likes of Thanos and Darkseid when it comes to being a hulking Invincible Villain. In the film Apocalypse is... just another powerful Mutant, but worse still he's smaller, Ivan Ooze-esque and his molecule controlling powers are undefined, underused and inconsistent. It's pretty egregious in the Final Battle where he's telepathically matched by Professor X and then destroyed by Combination Attack of the X-Men and Jean's Phoenix Force powers. For reference in the comics when the X-Men and The Inhumans (including Black Bolt who can shatter planets with his voice) did a similar combined attack against Apocalypse, and it was reduced to The Worf Barrage as Apocalypse just tanked it◊.
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