- Fridge Horror: Snape made a Horcrux during his late teens (a Horcrux Voldemort is now using to blackmail him). Which means he killed an innocent in cold blood and has never regretted it.
- Fridge Logic: Professor Snape considers several ideas about the Muggle world (man reaching the Moon, atomic bombs, dinosaurs) preposterous or nonsense. However, he lived in the Muggle world for all his early life and good part of his teen phase (he was 9 when the Apollo 11 landings took place), so he should have learned all about it, if not directly, then through Lily.
- "Funny Aneurysm" Moment: The disclaimer to Chapter 5 has Alyx saying "Please ignore Bob screaming. He must die, really, it's for the Greater Good". Bob died of cancer in April 2016.
- Narm: there are several parts of the story that are a bit cringe-worthy.
- Never Live It Down: Professor McGonagall ignoring Harry when he complained over what Umbridge was doing to him (never mind that this did not happen in the books).
- Ron the Death Eater: Downplayed with the Trope Namer, who develops an irrational dislike of mutants out of nowhere and becomes jealous and/or angry with Harry, but he later apologizes to Harry, obviously not expecting forgiveness (which Harry gives).
- Played more straight with Dumbledore, who, while opposed to Voldemort, is willing to give Death Eaters free rein with the hope that they will repent on their own while berating Harry for defending himself.
- To the hilt with Snape. A lot more obnoxious than in the books, he used the Occlumency lessons to Mind Rape Harry without opposition, supports Voldemort (although not entirely willingly) and proves to be an unrepentant anti-Muggle bigot. See Fridge Horror for more on the issue.
- They Wasted a Perfectly Good Plot: not the story itself, which is good, but Harry's magical tattoo of a dragon, which, according to Hagrid, would ensure that dragons considered Harry a friend and probably give him some abilities. They had a chance to make an awesome subplot out of it, and nothing came! Though, it could be said that The Queen Who Fell To Earth delivered on that promise.
- Voldemort mentions using mutants in the same way werewolves are (i.e. Cannon Fodder). The chance to have a meeting between Magneto (who gets mentioned only twice in the entire story) and Voldemort is there, but it never happens.
YMMV / Mutant Storm