I'll certainly accept that Season 3 didn't contradict anything. But it did ignore the Season 2 storyline, apart from one offhand, dismissive mention from Shaw early on. That's not a problem for continuity. And it's not a problem for anyone who didn't want to see the Season 2 stuff explored further. It was a problem for me because I would have found further exploration of it interesting, more interesting than what Season 3 did with the Borg.
Again with "Unimatrix Zero," my point is that they did no further stories about the Borg rebellion. Again, not a problem with continuity. Not a problem for anyone who didn't want those stories. I did.