- Ass Pull: Beast defeats Danger and Ord by immobilizing them with a giant magnet. Said apparatus had never been mentioned in any of the previous issues, and it inexplicably has no effect on Wolverine despite him standing in the same location and having a skeleton coated in metal.
- Broken Base: The series is generally well liked, but there's a few things that people debate on to this day.
- Primarily, some people dislike the focus given to Kitty. Given Joss' well-known love of her character, some found it annoying and felt it made her a Creator's Pet. Others, however, liked that someone wanted to use her again after she'd spent so much time off-the-radar.
- Pairing Kitty with Colossus once again, especially given their sex scene, also turns some people off due to the implications it brings if they assume Colossus is being used as an Author Avatar. It doesn't help that some confuse the scene for being Kitty losing her virginity, when rather it was merely the first time the two had slept with each other. It helps that Whedon's not the first writer to put in a sex scene between Kitty and an Author Avatar (Warren Ellis, the man who'd take over the title after Whedon, did so in his Excalibur run).
- The World of Snark going around in the series. Some felt it was out of character for Cyclops and Wolverine to be snarky, while others point at previous points when the two snarked, or noted that it was a nice addition. Then there's some that just resent it for being such a Whedony trait and how abundant it was.
- Crazy Is Cool: When Cyclops suffers Mind Rape by the hands of Emma, he awakens with his powers temporarily under control, and he has no problem with taking a gun, blowing the brains out of the psychic projections of the Hellfire Club, while happily telling Peter that, as an X-Man, he doesn't shoot people, he's merely making a point.
- Fridge Logic: It's established in "Unstoppable" that Danger is incapable of killing anyone. However, this contradicts events from her first battle against the X-Men, in which Cyclops would have died from his injuries had Kitty not performed CPR on him; and Danger has no problems lethally impaling Colossus and Shadowcat.
- Hype Backlash: More than one comic site considers Whedon's full run to be one of the best, if not the best X-Men run of all time. More than one fan finds these claims grossly inaccurate, and will argue all the books' faults as well as their faults with Whedon in general.
- Jerkass Woobie: Kaga may be a genocidal, hateful maniac, but you can't exactly blame him for being so bitter after his backstory. And the X-Men's borderline-No Sympathy reaction to his Motive Rant only increases this.
- Strawman Has a Point: Dr. Kavita Rao develops a way to suppress the X-gene which causes mutations and declares it a "cure" for mutants. The X-Men are disgusted by this line of thinking, insisting that the mutant community should stick together and refuse to take the drug on principle. However, they're a team of conventionally-attractive (with the exception of Beast, but even he is still muscular and humanoid) superheroes with strong control over their useful mutant gifts and a ton of resources. The majority of the mutants who do want the cure are either physically deformed in some way—we see a man whose torso is also his head, a fly-like creature, a ghostly teenager who lacks a body, and a boy with crab claws, among others—or suffer from incredibly dangerous Power Incontinence (Dr. Rao was inspired to work on the cure by a little girl she adopted who has the ability to subconsciously bring her nightmares to life, which in turn killed her birth parents). Given that those people are clearly suffering both physical and mental anguish from their mutations, it's hard not to support Dr. Rao's attempts to help them, even if dubbing mutation overall as an illness is a narrow-minded view.
- Tear Jerker: The aftermath of Kitty's phasing the giant bullet through the earth. Cyclops regretfully tells Colossus that there's no way for them to bring Kitty back.
- The giant bullet that's fired from the Breakworld to destroy the Earth has magical defenses that trap the planet's heroes in a dreamlike trance to prevent them from interfering. Spider-Man is the first to awaken from the spell, and he desperately attempts to snap the others out of it as the bullet gets closer and closer. When all seems lost, the teenage hero quietly cries "Somebody please do some magic..."
- Unintentionally Unsympathetic: Some see the X-Men as this after their Cruel Mercy against Kaga, considering his entire life has been preemptive Laser-Guided Karma in and of itself. Wolverine (the poster-boy for Healing Factor and Made of Indestructium) in particular even punches him (a known-frail Muggle) unconscious — after his Villainous BSoD-induced surrender, no less. It can just come across as an unpleasant (and, more importantly, dangerous — given a still-alive Kaga could possibly (however slightly) escape to invoke another Roaring Rampage of Revenge) Kick Them While They Are Down.
- Their borderline No Sympathy reaction only further enhances this. Sure, the X-Men are feared and hated by normal human society, but compared to Kaga and the Morlocks, it's hard not to think that the X-Men really lucked out as far as mutations go. It makes them come across as bigger jerks than what the audience were expecting.
YMMV / Astonishing X-Men