These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Author's Saving Throw: Done in the simplest possible way to remove the revelation that Northstar and Aurora were half-elven: that story came from Loki, and Loki lies.
Creator Backlash: John Byrne against his successor, Bill Mantlo. While he was never fond of the idea of putting Heather into Mac's battlesuit, Byrne was especially upset with the handling of Puck. Byrne had always intended Puck to be a dwarf naturally, due to achondroplasia, and the pain he suffered is a legitimate side-effect of that condition. Instead, Mantlo introduced the concept of Puck being a mystic prison for a demon, and his dwarfism was the result of that curse. Though Mantlo shouldn't be held entirely responsible for the concept; Chris Claremont introduced the "curse" aspect (and Judd's "true" height) in the X-Men/Alpha Flight miniseries; Mantlo simply came up with the explanation for it.
Fanon Discontinuity: Every Alpha Flight story after the original series, save for the brief Omega Flight series, which did it's best to undo Bendis's slaughter of the team by way of revealing Sasquatch survived "The Collective" and only stating outright, that the two least liked Alphas (James MacDonald Hudson and Shaman) were dead.
Flat Character: Creator John Byrne felt this way about the majority of the team, especially Mac, which is why Guardian was killed so early into his run. The only exception would be Northstar and Aurora and, to a lesser extent, Heather Hudson.
This is also why many fans consider Bill Mantlo to be the real father of the series. The definitive take on the bulk of the cast were the result of Mantlo fleshing out the characters into three-dimensional people.
Probably because Canada is evil in the Marvel universe.
Alternately, Canadians are very used to American media, and so tend to have a very negative opinion of American media portrayals of Canada and Canadian cultures (see Dudley Do-Right). A newcomer to the comic would suspect that, since Marvel is an American company, Alpha Flight would be a continuation of those stereotypes. So, like any stereotype, best to be avoided, and certainly not a good basis for a comic series. It doesn't help that, in a lot of Alpha Flight's guest appearances in other books, all they do is play up those roles (when they're not unexpected antagonists). Plus most Canadians only like jokes about Canada when we tell them (because we doitright).
The Woobie: Despite his killing the previous team while possessed by Xorn and it being explicitly not his fault, the third Guardian is treated as if he's a psychotic criminal.
Poor Marrina. So, so much.
Marrina stopped being the woobie in volume four, when Fred Van Lente recast her as no longer giving a fuck about humanity after being brought back to life. Arguably the only redeemable thing from the Van Lente series many would argue.