Not necessarily, Quicksilver's inclusion in both films proves that there are grey areas, that just because a character was used in one franchise doesn't mean they (or their name) are automatically off-limits in another. It just depends on if the Hudsons are considered to essentially be Wolverine supporting cast, or if Alpha Flight is its own entity independent of the X-Men books they debuted in. And until explicitly told otherwise, I CHOOSE TO BELIEVE.
The mutant thing is true, but there are any number of easy excuses they could make for the twins to have powers, I wouldn't really call it a problem.
Department H exists in the Marvel Cinematic Universe, that has to be worth something, right?