- Author's Saving Throw: The writer of the new series has promised that the Chamber and Husk relationship won't be picked up again.
- Base-Breaking Character: Quentin Quire being a member of the 2017 incarnation have divided fans with some not minding and others not happy given the fact that Quire was depicted as a Jerkass during Morrison era New X-Men and Aaron era Wolverine and the X-Men. Not helped by the fact that he's a Base-Breaking Character among longtime fans of the main X-titles.
- Bizarro Episode: The storyline in the 30s where the M twins and Emplate merged into a single entity and pursued some pandimensional MacGuffin that turned out to be a Barrier Maiden. The team chased them on a cartoonish train with help from a talking rabbit. The storyline began with an attempt to explain the St. Croix family secrets, but quickly veered off into Alice in Wonderland territory.
- Complete Monster: Johnston Coffin, from 2000's "Correction" storyline, is wanted by S.H.I.E.L.D. for crimes against humanity, but instead somehow finds himself employed by the US Government. With the government's blessing, he builds a Hellhole Prison where he "fixes" disobedient teenagers, many of which had only said or thought something disobedient. He also has his "Special Children"—kids from his first prison in the '70s, whom he's wired up to huge cyborg bodies and uses as security. They've been that way so long—it's implied in perpetual agony—that their bodies have actually begun to rot. He also has half a human mounted on his wall, is implied to be a rapist, and carries around the skull of a child he shot in the head everywhere he goes.
- Franchise Original Sin: Aimlessness. A majority of the time, the book had no solid plot plans or even a solid idea of what the characters were doing. For the first half of the series, this wasn't so bad because the character-based plots and interactions held everything together. As it went on, the good parts fell away one by one, and the lack of a solid direction to go into left the writers floundering and the readers annoyed.
- Hilarious in Hindsight: Before growing closer in their shared grief of Everett, Jubilee & Monet's rivalry counts due to the men they're close with.
- Another when Jubilee has a nightmare where Freddy Krueger Sabretooth murders Skin & M. Again, funny to see when you look at the relationship Creed & M eventually end up having.
- Nightmare Fuel: Everything about Johnston Coffin. His men can come for you at any time, simply for doing something like insulting the school principal, he'll lock you up for the rest of your life, and if he gets you, having your head squashed like a grape is only the second-worst thing that can happen to you. Oh, and he claims to be an abstract concept in human form, so it's entirely possible he's unkillable. He may just be a powerful mutant, though.
- Romantic Plot Tumor: Chamber and Husk's on-and-off-but-was-never-really-on-to-begin-with relationship. Chamber's Wangst and the Token Minority Couple feel of it (they were the only white students) certainly didn't help either. Even worse was when the series ended and the arguing carried into Uncanny X-Men at the most inappropriate moments, such as the team's fight against Alpha Flight. Thankfully, the writer of the new volume says this plot thread won't carry over despite both of them showing up as supporting characters.
- Seasonal Rot: The Larry Hama run on the book (which aimed for surreal but ended up with a series of Bizarro Episodes), as well as the writer who came after.
- Not quite. Hama's succesor Jay Faerber was actually rather well received in comparison.
- Wangst: While generally justified, Chamber approached this at times.
YMMV / Generation X