That aren't related to Alpha Flight....But I talk about them a lot, so...

I think I finally know why the X-Men attacked the Hellions and arrested them:
1. According to "It Only Hurts When I Cry", The Hellions were being trained by agents of Apocalypse, making them "collaborators" to some extent.
and
2. It was the X-Men's first outing as government hounds and the media was there, so they chose the weakest possible foes they could find and caught them off guard so they could be assured a "spectacular victory..."

I still think it was cowardly.
So you're sitting in an abandoned school watching cartoons, and the X-Men come out of nowhere, beat the crap out of you and throw you in jail....

What's funny is, they busted Cyclops too, and he betrayed Apocalypse and almost died trying to help rescue people from the Pens...

As much as I hate to say it though... they're all probably safer in jail than out among an understandably angry human population who (wrongly)want mutant blood and don't care who it comes from...