- 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 Awesome: 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.
- Fandom Rivalry: With fans of Grant Morrison's New X-Men. Given that Astonishing X-Men and New X-Men take practically polar opposite approaches to the mythos, it's understandable.
- 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.
- TearJerker: 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.
- 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