The deaths (or apparent deaths) of Kathryn Janeway and Montgomery Scott.
Between sudden abrupt shifts in characterization of the new characters introduced in the previous two booksnote to the point where it was blatantly obvious that Peter David hadn't communicated with the other authors whatsoever - for instance, one happily-married character was suddenly lusting after the new security chief, who was most definitely NOT her husband, the death of Janeway, and, in the eyes of some readers, a ludicrous plot, "Before Dishonor" was not well received by a good chunk of the fandom.
Also counts as a Continuity Nod to the older novel Vendetta which featured the completed version of the thing. You read that right. The one in The Doomsday Machine was theorized in Vendetta to be a PROTOTYPE that was launched because the war between the creators of the original machine and the Borg was going badly for the good guys. This series outright confirms the theory established years ago by Vendettanote Of course, since both were written by Peter David, Your Mileage May Vary. The final version went into something like Warp 9.999999999999-ad infinitum (Warp 10 was still "unreachable" at the time Peter David wrote the novelnote Your Mileage May Vary if it still is or not, given that the Voyager episode Threshold has largely been written out of continuity), with its pilot, linked to the minds of the ship (essentially making the ship a sentient collective- the irony abounds) intending to go straight for the Borg homeworld and devour it before she died of phaser wounds that should have been fatal.
Picard and the Enterprise hooking up unexpectedly with none other than Mackenzie Calhoun and theExcalibur, who then proceeds to declare Picard honorary commodore of his and the other ships as they head out to engage the Borg.