Seven's parents were apparently out in space investigating the Borg 15 years before the events of "Q Who." That one gives me a big.
Why? Q implied the Borg was something Picard should have been aware of already.
No, not really. At least that's not the impression I got. In Q Who Q basically gets tired of Picard's arrogant attitude, so to put Picard in his place, Q pits the Enterprise against an enemy powerful enough to destroy them. That's it, no hidden agenda to make the Federation aware of the Borg, nothing of the sort. Just teaching a crew of arrogant and complacent SOBs that they're not invincible.
As for Annika's parents investigating a mysterious alien race for years, it's easy enough to accept it as being based on very sketchy evidence. They didn't have a very good idea of what they were after until it was too late--their first direct encounter with the Borg resulted in their assimilation. Although "Q" is incredibly powerful, he doesn't know the goings on of each individual life form throughout the galaxy (if he did, then well, you could really call him a God). I presume "Q" was ignorant of Annika's parents.
The only other thing difficult to resolve is that once Annika and her parents were assimilated, the Borg would know of the Federation and already be on the hunt... correct? Could "Q" read the minds of the Borg and know what they knew? I wonder...
So "Q" makes the Federation aware of the Borg in response to Picard's apparent arrogance, in turn making the Borg aware of the Federation. That's an extremely significant form of manipulation. "Q" did say that it was only a matter of time before they encountered the Borg, so he just stepped up the timeline a little faster. Well, that's pretty intrusive and seemingly outside the boundaries of what the continuum would normally do (inferred from what "Q" has said, anyway). And it wasn't that much later when the Borg began their intrusion into the Alpha quadrant. "Q" could have at least erased all memory of the Federation from the Borg's consciousness, giving the Federation a little more time to prepare for the inevitable.
The other issue is how the Borg are presented. I do not feel like the Queen was in keeping with the personification of the Borg. The whole premise behind them was a lack of an individual, being one massive collective. And they realized that due to the individualistic nature of the Federation, they had to kidnap someone to become a kind of liaison (Locutus). If they had a Queen, there would be no need for that. She operated like an individual. One could argue that the Borg are very adaptive and perhaps their exposure to the powerful Federation had them try out this concept of a centralized figure within their collective... a kind of hybridization of two forms of social governance. But no... they went back and gave Picard memories of interfacing with the Borg Queen.

Anyway, you have this very significant first introduction of the Borg in TNG, only to punch a major hole through it with the Borg appearing in Enterprise. That to me is the best example of canon violation, and probably the only thing I really have a beef with. A lot of the other conflicts in continuity are easy enough to overlook.
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